Variant report

Variant	rs57820533
Chromosome Location	chr3:195621286-195621287
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:195621083-195624613	SK-N-SH	brain:	n/a	chr3:195622552-195622562 chr3:195622031-195622041 chr3:195623099-195623106 chr3:195621649-195621663 chr3:195621274-195621284 chr3:195622712-195622722
2	RAD21	chr3:195621014-195622371	SK-N-SH	brain:	n/a	chr3:195622017-195622030 chr3:195621986-195621996 chr3:195622031-195622041 chr3:195621647-195621659 chr3:195621645-195621664 chr3:195621649-195621659 chr3:195622031-195622043 chr3:195622029-195622042
3	CTCF	chr3:195621249-195622425	HCT-116	colon:	n/a	chr3:195621648-195621664 chr3:195622028-195622041 chr3:195621647-195621665 chr3:195621642-195621663 chr3:195621649-195621662 chr3:195622369-195622382
4	MXI1	chr3:195621231-195624633	SK-N-SH	brain:	n/a	chr3:195622762-195622771
5	HCFC1	chr3:195621145-195623684	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr3:195620875-195624618	IMR90	lung:	n/a	chr3:195620987-195620996
7	MXI1	chr3:195621105-195624625	IMR90	lung:	n/a	chr3:195622762-195622771
8	CTCF	chr3:195621180-195621330	GM12874	blood:	n/a	n/a
9	NR2F2	chr3:195621273-195622322	K562	blood:	n/a	n/a
10	CTCF	chr3:195621140-195621290	GM12864	blood:	n/a	n/a
11	RAD21	chr3:195621241-195622307	HCT-116	colon:	n/a	chr3:195622017-195622030 chr3:195621986-195621996 chr3:195622031-195622041 chr3:195621647-195621659 chr3:195621645-195621664 chr3:195621649-195621659 chr3:195622031-195622043 chr3:195622029-195622042
12	CTCF	chr3:195620924-195622656	SK-N-SH	brain:	n/a	chr3:195621648-195621664 chr3:195622028-195622041 chr3:195621647-195621665 chr3:195621642-195621663 chr3:195621649-195621662 chr3:195622369-195622382

No.	Distal block	Cell Line	Cell type
1	chr3:195620885..195622532-chr3:195635337..195638039,2	K562	blood:
2	chr3:195615420..195617360-chr3:195618716..195622167,3	MCF-7	breast:
3	chr3:195620748..195623057-chr3:195678515..195681386,2	K562	blood:
4	chr3:195585687..195591910-chr3:195617865..195621709,8	K562	blood:
5	chr3:195583683..195587914-chr3:195619199..195624309,6	K562	blood:
6	chr3:195614947..195618146-chr3:195619522..195621425,3	MCF-7	breast:

Variant related genes	Relation type
TNK2	TF binding region
ENSG00000260261	Chromatin interaction
ENSG00000061938	Chromatin interaction
ENSG00000223783	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2086358	0.88[AFR][1000 genomes]
rs61248803	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62284390	1.00[ASN][1000 genomes]
rs62284418	1.00[ASN][1000 genomes]
rs6762607	0.83[AFR][1000 genomes]
rs6805088	0.80[EUR][1000 genomes]
rs73087325	1.00[ASN][1000 genomes]
rs73087353	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
2	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1001387	chr3:195186128-195661538	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
5	nsv428102	chr3:195201080-195829426	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv428430	chr3:195201080-195829426	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv1006217	chr3:195312401-195643229	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv536882	chr3:195312401-195643229	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
9	esv1813494	chr3:195325408-195628669	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
11	nsv1006165	chr3:195383130-195777211	Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv471621	chr3:195417664-195795474	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv878157	chr3:195421983-195628636	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
14	esv2751988	chr3:195433543-195651349	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
15	esv2756651	chr3:195433543-195696720	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
16	nsv432528	chr3:195433543-195696720	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
17	esv2754016	chr3:195433543-195753766	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
18	nsv822410	chr3:195438740-195725565	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
19	nsv1003062	chr3:195473784-195630700	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
20	nsv878162	chr3:195475989-195641908	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
21	nsv878163	chr3:195477791-195641908	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
22	nsv997893	chr3:195501392-195642192	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
23	nsv1005193	chr3:195526571-195709662	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
24	nsv878166	chr3:195550366-195628636	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
25	nsv878167	chr3:195550366-195637439	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
26	nsv878168	chr3:195553259-195644332	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
27	nsv1002591	chr3:195564086-195643229	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
28	nsv530397	chr3:195565159-195740416	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
29	nsv878169	chr3:195571024-195628636	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
30	nsv593056	chr3:195571024-195656731	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
31	nsv1007235	chr3:195582468-195651911	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
32	nsv1002629	chr3:195582468-195769275	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
33	esv1811906	chr3:195598137-195637469	Active TSS Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
34	esv1803133	chr3:195606770-195623789	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
35	nsv1014602	chr3:195606770-195661538	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
36	nsv829827	chr3:195608866-195760829	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195589400-195621800	Weak transcription	Small Intestine	intestine
2	chr3:195604800-195621600	Weak transcription	A549	lung
3	chr3:195612800-195621800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:195613600-195621600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:195617600-195624400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr3:195618400-195621400	Enhancers	Placenta	Placenta
7	chr3:195618400-195621600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:195618400-195621600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:195618600-195621600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:195618600-195621600	Enhancers	Fetal Brain Male	brain
11	chr3:195618800-195621400	Enhancers	Pancreas	Pancrea
12	chr3:195618800-195621600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr3:195619000-195622000	Enhancers	Gastric	stomach
14	chr3:195619200-195621600	Weak transcription	Fetal Kidney	kidney
15	chr3:195619200-195621600	Enhancers	Lung	lung
16	chr3:195619200-195621800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:195619400-195621600	Weak transcription	Primary T cells from cord blood	blood
18	chr3:195619400-195621600	Enhancers	Fetal Heart	heart
19	chr3:195619400-195621600	Enhancers	Stomach Mucosa	stomach
20	chr3:195619400-195621800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:195619400-195622600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:195619600-195621400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:195619600-195621400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr3:195619600-195621600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:195619600-195621800	Weak transcription	Aorta	Aorta
26	chr3:195619800-195621400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:195619800-195621400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:195619800-195621600	Enhancers	Primary hematopoietic stem cells	blood
29	chr3:195619800-195621600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr3:195620000-195621400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:195620000-195621400	Enhancers	Primary B cells from peripheral blood	blood
32	chr3:195620000-195621400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr3:195620000-195621400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:195620000-195621400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:195620000-195621400	Enhancers	Fetal Intestine Large	intestine
36	chr3:195620000-195621400	Enhancers	Fetal Intestine Small	intestine
37	chr3:195620000-195621400	Enhancers	Fetal Stomach	stomach
38	chr3:195620000-195621600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:195620000-195621600	Enhancers	Primary B cells from cord blood	blood
40	chr3:195620000-195621600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:195620000-195621600	Enhancers	Liver	Liver
42	chr3:195620000-195621600	Enhancers	Fetal Lung	lung
43	chr3:195620000-195621600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:195620000-195621600	Enhancers	Thymus	Thymus
45	chr3:195620000-195621800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:195620000-195621800	Enhancers	Right Atrium	heart
47	chr3:195620200-195621400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr3:195620200-195621400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:195620200-195621400	Enhancers	Colonic Mucosa	Colon
50	chr3:195620200-195621400	Enhancers	Duodenum Smooth Muscle	Duodenum

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