Variant report

Variant	rs72932925
Chromosome Location	chr3:50295399-50295400
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50295225-50295577	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:50295241-50295670	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:50295346-50295575	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:50294093-50295852	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:50295360-50295775	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:50294100-50296266	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:50295223-50295525	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:50295332-50295440	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:50295223-50295682	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:50295246-50295514	K562	blood:	n/a	n/a
11	MYC	chr3:50295332-50295529	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr3:50295302-50296681	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:50295222-50295931	GM12892	blood:	n/a	n/a
14	POLR2A	chr3:50295220-50295483	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:50294296-50295828	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:50295292-50295416	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:50295349-50295405	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:50295219-50298815	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:50295253-50295545	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:50295248-50295878	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:50293586-50295957	HL-60	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50266710..50270196-chr3:50295064..50299749,5	K562	blood:
2	chr3:50291997..50295519-chr3:50296180..50299303,4	MCF-7	breast:
3	chr3:50293747..50295970-chr3:50606767..50608442,2	MCF-7	breast:
4	chr3:50288957..50291643-chr3:50295341..50296878,2	K562	blood:
5	chr3:50294811..50297439-chr3:50365376..50367320,3	MCF-7	breast:
6	chr3:50275833..50279919-chr3:50292841..50298987,5	MCF-7	breast:
7	chr3:50294632..50297362-chr3:50310671..50313521,2	K562	blood:
8	chr3:50283167..50285280-chr3:50294305..50297270,3	MCF-7	breast:
9	chr3:50290143..50293966-chr3:50294360..50298503,5	K562	blood:
10	chr3:50294678..50296815-chr3:50329607..50331769,2	K562	blood:
11	chr3:50272477..50276068-chr3:50288828..50297512,10	MCF-7	breast:
12	chr3:50292125..50293966-chr3:50295138..50298503,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000230454	TF binding region
ENSG00000114735	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000213600	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000114383	Chromatin interaction
ENSG00000214706	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17050913	1.00[AMR][1000 genomes]
rs17050922	1.00[AMR][1000 genomes]
rs58124375	1.00[AMR][1000 genomes]
rs58407586	1.00[AMR][1000 genomes]
rs59112948	1.00[AMR][1000 genomes]
rs60564525	1.00[AMR][1000 genomes]
rs72931482	1.00[AMR][1000 genomes]
rs72932915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932918	1.00[AMR][1000 genomes]
rs72932949	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72932994	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934811	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936964	1.00[AMR][1000 genomes]
rs72936978	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938724	1.00[AMR][1000 genomes]
rs72938734	1.00[AMR][1000 genomes]
rs72938735	1.00[AMR][1000 genomes]
rs72938738	1.00[AMR][1000 genomes]
rs72938740	1.00[AMR][1000 genomes]
rs72938750	1.00[AMR][1000 genomes]
rs7611074	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
7	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
11	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic 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	103 gene(s)	inside rSNPs	diseases
12	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
20	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
21	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
25	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
26	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
27	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
28	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50284200-50297000	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:50284400-50295800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:50284400-50297000	Genic enhancers	Fetal Muscle Leg	muscle
4	chr3:50284800-50300600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:50285200-50296000	Strong transcription	Dnd41	blood
6	chr3:50285200-50296600	Strong transcription	Thymus	Thymus
7	chr3:50286000-50296200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:50286800-50297000	Weak transcription	A549	lung
9	chr3:50287200-50296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:50287600-50295400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:50287800-50297200	Weak transcription	Small Intestine	intestine
12	chr3:50288200-50295600	Strong transcription	Fetal Thymus	thymus
13	chr3:50288600-50296200	Strong transcription	Primary T cells from cord blood	blood
14	chr3:50288600-50296600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:50288800-50295800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:50288800-50296000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:50289000-50296000	Strong transcription	Rectal Smooth Muscle	rectum
18	chr3:50289000-50296200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr3:50289000-50296200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:50289000-50296400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:50289000-50297000	Weak transcription	Fetal Heart	heart
22	chr3:50289000-50297000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:50289000-50297600	Genic enhancers	HUVEC	blood vessel
24	chr3:50289200-50296000	Strong transcription	Colonic Mucosa	Colon
25	chr3:50289400-50296000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:50289400-50297000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:50289400-50297000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:50289400-50297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:50289600-50296200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:50289600-50296200	Strong transcription	Ovary	ovary
31	chr3:50289800-50296400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:50289800-50296600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:50290000-50296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:50290400-50295800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:50290600-50297000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:50291200-50295600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:50291200-50296200	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr3:50291600-50296000	Genic enhancers	Brain Anterior Caudate	brain
39	chr3:50291600-50296800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:50292000-50295400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:50292400-50295800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:50292400-50296200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:50292400-50296600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:50292600-50295800	Strong transcription	Fetal Brain Female	brain
45	chr3:50292600-50296800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:50292600-50297000	Strong transcription	NHLF	lung
47	chr3:50292800-50296600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:50292800-50296600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:50292800-50296600	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr3:50292800-50296800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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