Variant report

Variant	rs17006713
Chromosome Location	chr3:20228844-20228845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:20226840-20229172	GM18505	blood:	n/a	n/a
2	TBL1XR1	chr3:20227079-20228974	K562	blood:	n/a	n/a
3	POLR2A	chr3:20226822-20229091	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:20227401-20228857	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:20226441-20229232	GM19099	blood:	n/a	n/a
6	POLR2A	chr3:20226769-20229489	GM12878	blood:	n/a	n/a
7	MXI1	chr3:20226632-20229279	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:20226431-20229063	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:20226670-20229394	GM12891	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:20227831..20229515-chr3:20229924..20231692,2	MCF-7	breast:
2	chr3:20197490..20199260-chr3:20227955..20230018,2	K562	blood:
3	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
4	chr3:20225377..20229978-chr3:20232761..20235716,5	K562	blood:
5	chr3:20213813..20216501-chr3:20227432..20229116,2	MCF-7	breast:
6	chr3:20226448..20228980-chr3:20231144..20234755,4	MCF-7	breast:
7	chr3:20212661..20217850-chr3:20224065..20229766,9	K562	blood:
8	chr3:20228018..20229588-chr3:20240700..20242261,2	K562	blood:
9	chr3:20094893..20096727-chr3:20227964..20230863,2	MCF-7	breast:
10	chr3:20079279..20082964-chr3:20226299..20229620,6	K562	blood:
11	chr3:20219250..20222131-chr3:20228592..20230370,2	K562	blood:
12	chr3:20079527..20082964-chr3:20226742..20229620,4	K562	blood:
13	chr3:20227937..20230614-chr3:20238703..20240365,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KAT2B-1	chr3:20227726-20230848	NONHSAT088617

No data

Variant related genes	Relation type
SGOL1	TF binding region
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000237485	Chromatin interaction
ENSG00000252442	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000114166	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510500	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11925947	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11926045	1.00[EUR][1000 genomes]
rs17006540	1.00[EUR][1000 genomes]
rs17006672	1.00[EUR][1000 genomes]
rs17006691	1.00[EUR][1000 genomes]
rs17006697	1.00[EUR][1000 genomes]
rs17006709	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17006737	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17006767	1.00[EUR][1000 genomes]
rs17006783	1.00[EUR][1000 genomes]
rs2068668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655370	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3901613	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4395419	1.00[EUR][1000 genomes]
rs56908553	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58969372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59044146	1.00[EUR][1000 genomes]
rs60640011	1.00[EUR][1000 genomes]
rs60985112	1.00[EUR][1000 genomes]
rs61004804	1.00[EUR][1000 genomes]
rs6550356	1.00[EUR][1000 genomes]
rs6550363	1.00[EUR][1000 genomes]
rs6550365	1.00[EUR][1000 genomes]
rs6770067	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6799600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6802066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803142	1.00[EUR][1000 genomes]
rs6806621	1.00[EUR][1000 genomes]
rs6807071	1.00[EUR][1000 genomes]
rs6808308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6810209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7616513	1.00[EUR][1000 genomes]
rs7642627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650577	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	esv1831853	chr3:20157077-20615273	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	esv1833208	chr3:20157077-20638228	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	esv2422249	chr3:20163608-20626956	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv1826144	chr3:20164282-20638228	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	nsv1013532	chr3:20172889-20305612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv536513	chr3:20172889-20305612	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
21	esv1831289	chr3:20191506-20617984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	esv1829973	chr3:20192578-20375260	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
23	esv1829847	chr3:20196923-20638228	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	nsv876597	chr3:20197364-20242143	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	esv1829457	chr3:20200232-20375260	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	esv1830113	chr3:20200232-20430932	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
27	esv3377463	chr3:20203472-20343029	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	esv3381923	chr3:20203492-20342999	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	esv3322354	chr3:20228442-20229010	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20224600-20229000	Active TSS	GM12878-XiMat	blood
2	chr3:20225800-20229000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:20226000-20229000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:20226000-20229000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:20226000-20229000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:20226200-20229000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:20226200-20229200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:20226200-20229200	Active TSS	NHLF	lung
9	chr3:20226400-20229000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:20226400-20229000	Active TSS	Fetal Intestine Large	intestine
11	chr3:20226400-20229200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:20226600-20229000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:20226600-20229000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:20226600-20229600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:20226800-20229000	Active TSS	Fetal Intestine Small	intestine
16	chr3:20226800-20229200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:20227000-20229000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:20227000-20229200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:20227200-20229000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:20227200-20229600	Active TSS	Ovary	ovary
21	chr3:20227600-20229000	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:20227800-20229000	Active TSS	Right Atrium	heart
23	chr3:20228000-20229000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:20228200-20229000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr3:20228200-20229000	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr3:20228200-20229000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr3:20228200-20229000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:20228200-20229000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:20228200-20229000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr3:20228200-20229000	Flanking Active TSS	HUVEC	blood vessel
31	chr3:20228200-20229200	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr3:20228200-20229200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:20228200-20229200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr3:20228200-20229200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:20228200-20229200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:20228200-20229200	Active TSS	Brain Germinal Matrix	brain
37	chr3:20228200-20229400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr3:20228200-20229400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr3:20228400-20229000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:20228400-20229000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:20228400-20229000	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr3:20228400-20229000	Enhancers	Fetal Heart	heart
43	chr3:20228400-20229000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:20228400-20229000	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr3:20228400-20229200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:20228400-20229200	Active TSS	Stomach Smooth Muscle	stomach
47	chr3:20228400-20229200	Flanking Active TSS	Hela-S3	cervix
48	chr3:20228400-20229400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr3:20228400-20229400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:20228400-20239400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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