Variant report

Variant	rs2061099
Chromosome Location	chr12:123349070-123349071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr12:123348832-123350028	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:123349041-123349263	ProgFib	skin:	n/a	n/a
3	BCL3	chr12:123348905-123350084	K562	blood:	n/a	chr12:123349145-123349154
4	POLR2A	chr12:123346635-123351620	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:123348652-123351900	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:123344450-123350810	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr12:123345760-123350857	K562	blood:	n/a	n/a
8	POLR2A	chr12:123347500-123350770	GM19193	blood:	n/a	n/a
9	MTA3	chr12:123349014-123349877	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:123348669-123353259	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr12:123348679-123349941	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:123348679-123350841	GM12891	blood:	n/a	n/a
13	POLR2A	chr12:123348685-123350836	K562	blood:	n/a	n/a
14	POLR2A	chr12:123348702-123350727	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr12:123348690-123350909	MCF-7	breast:	n/a	n/a
16	POLR2A	chr12:123349048-123349847	GM12891	blood:	n/a	n/a
17	POLR2A	chr12:123348813-123350855	A549	lung:	n/a	n/a
18	POLR2A	chr12:123348726-123349319	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr12:123348575-123349998	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr12:123348733-123349239	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr12:123349053-123349364	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:123348764-123349080	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:123344139-123350814	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr12:123349053-123349393	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:123348637-123350155	K562	blood:	n/a	n/a
26	POLR2A	chr12:123348674-123350702	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr12:123349064-123349397	A549	lung:	n/a	n/a
28	ESR1	chr12:123348995-123349273	T-47D	breast:	n/a	chr12:123349168-123349185 chr12:123349167-123349184
29	POLR2A	chr12:123349044-123349276	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:123348576-123350855	H1-neurons	neurons:	n/a	n/a
31	BCL3	chr12:123348698-123349233	A549	lung:	n/a	chr12:123349145-123349154
32	POLR2A	chr12:123348756-123350832	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:123348684-123350872	GM12891	blood:	n/a	n/a
34	POLR2A	chr12:123347447-123353394	K562	blood:	n/a	n/a
35	POLR2A	chr12:123348620-123350720	HCT-116	colon:	n/a	n/a
36	POLR2A	chr12:123349026-123351272	K562	blood:	n/a	n/a
37	POLR2A	chr12:123348609-123350093	HCT-116	colon:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:123347975..123349618-chr12:123459301..123462302,3	K562	blood:
2	chr12:123325084..123327709-chr12:123347219..123349157,2	MCF-7	breast:
3	chr12:123346730..123349618-chr12:123459301..123462302,3	K562	blood:
4	chr12:123348260..123351060-chr12:123715794..123718322,2	K562	blood:
5	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:
6	chr12:123331248..123334066-chr12:123346925..123349387,2	K562	blood:
7	chr12:123348287..123350765-chr12:123373068..123375043,2	MCF-7	breast:
8	chr12:123346271..123349232-chr12:123377793..123379796,2	K562	blood:
9	chr12:123346632..123349327-chr12:123372741..123374814,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000256152	TF binding region
ENSG00000130921	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000051825	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1026395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744394	0.88[EUR][1000 genomes]
rs10744439	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847742	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847749	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10847775	1.00[JPT][hapmap]
rs10847910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848148	1.00[JPT][hapmap]
rs10848363	1.00[JPT][hapmap]
rs10848365	1.00[JPT][hapmap]
rs11059729	0.86[CEU][hapmap]
rs11060152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060211	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11060932	1.00[JPT][hapmap]
rs11060999	1.00[JPT][hapmap]
rs11610441	1.00[MEX][hapmap]
rs12311043	1.00[JPT][hapmap]
rs1260121	1.00[JPT][hapmap]
rs1671684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1671686	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1671687	1.00[JPT][hapmap]
rs1696327	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1798563	1.00[JPT][hapmap]
rs1975761	1.00[JPT][hapmap]
rs2271048	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2343107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649895	1.00[JPT][hapmap]
rs2649896	1.00[JPT][hapmap]
rs2649903	1.00[JPT][hapmap]
rs2649904	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2656812	1.00[JPT][hapmap]
rs3844369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4307760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4759351	0.96[EUR][1000 genomes]
rs4759352	0.96[EUR][1000 genomes]
rs4759353	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759388	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap]
rs651683	1.00[JPT][hapmap]
rs7138257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298176	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306047	0.88[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7485652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957643	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs839354	1.00[JPT][hapmap]
rs897384	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs897388	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937765	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967281	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9795629	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised 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	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active 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 target site	15 gene(s)	inside rSNPs	diseases
7	nsv899575	chr12:123326374-123360151	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS 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 target site	11 gene(s)	inside rSNPs	diseases
8	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:123324800-123351600	Weak transcription	Small Intestine	intestine
5	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:123330400-123349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:123332600-123355600	Strong transcription	Thymus	Thymus
10	chr12:123337400-123356200	Weak transcription	Fetal Kidney	kidney
11	chr12:123337600-123351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:123337600-123351400	Weak transcription	HSMMtube	muscle
13	chr12:123337800-123351600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:123338400-123350400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:123338400-123351000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:123338800-123354200	Strong transcription	Brain Germinal Matrix	brain
17	chr12:123339000-123353200	Weak transcription	K562	blood
18	chr12:123339200-123354200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:123339600-123354200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:123339600-123355000	Strong transcription	Fetal Brain Female	brain
21	chr12:123341200-123350800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:123341200-123352200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:123342200-123350200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:123344000-123349200	Strong transcription	Primary T cells from cord blood	blood
25	chr12:123344400-123350600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:123344400-123351600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:123344400-123355000	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr12:123344600-123350600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:123344600-123350800	Weak transcription	Aorta	Aorta
30	chr12:123344600-123353000	Enhancers	Liver	Liver
31	chr12:123344800-123355200	Weak transcription	Hela-S3	cervix
32	chr12:123345000-123353600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:123345200-123352600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:123345200-123354000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:123345200-123355400	Weak transcription	Fetal Brain Male	brain
36	chr12:123345400-123350400	Weak transcription	Psoas Muscle	Psoas
37	chr12:123345400-123352200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:123345400-123353800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:123345400-123354400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:123345600-123351200	Weak transcription	GM12878-XiMat	blood
41	chr12:123345600-123355400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:123345800-123352800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:123345800-123354000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:123346200-123352800	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:123346400-123350000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:123346400-123352400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:123346600-123350600	Weak transcription	HUVEC	blood vessel
48	chr12:123346800-123350200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:123346800-123351400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:123347000-123351200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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