Variant report

Variant	rs3770086
Chromosome Location	chr2:86267278-86267279
allele	A/C
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	POLR2A	chr2:86267151-86267451	K562	blood:	n/a	n/a
2	POLR2A	chr2:86266947-86267290	K562	blood:	n/a	n/a
3	POLR2A	chr2:86267029-86267684	K562	blood:	n/a	n/a
4	POLR2A	chr2:86265726-86267954	K562	blood:	n/a	n/a
5	STAT3	chr2:86267218-86267331	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:86267089-86267721	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:86266326-86267980	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10184159	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11689889	0.86[CHB][hapmap]
rs12124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17026904	0.96[ASN][1000 genomes]
rs17579744	0.91[JPT][hapmap]
rs1978842	0.90[JPT][hapmap]
rs2278086	0.88[YRI][hapmap];0.96[AFR][1000 genomes]
rs2278532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278533	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278534	0.96[ASN][1000 genomes]
rs2278535	0.96[ASN][1000 genomes]
rs2278537	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2288116	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34302587	0.93[AFR][1000 genomes]
rs35093541	0.96[AFR][1000 genomes]
rs36051710	0.96[AFR][1000 genomes]
rs3731822	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755005	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770063	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3770064	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3770076	0.96[ASN][1000 genomes]
rs3770083	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770084	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770085	0.96[ASN][1000 genomes]
rs3770088	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3770091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821019	0.96[ASN][1000 genomes]
rs56673339	1.00[AFR][1000 genomes]
rs56861544	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57150140	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57318396	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57361751	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57405155	0.93[ASN][1000 genomes]
rs57906735	1.00[AFR][1000 genomes]
rs57963460	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58009603	0.96[ASN][1000 genomes]
rs58026145	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58403969	1.00[AFR][1000 genomes]
rs58429119	1.00[EUR][1000 genomes]
rs58614836	0.89[AFR][1000 genomes]
rs58810051	0.84[ASN][1000 genomes]
rs58861315	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58913632	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58919291	0.96[ASN][1000 genomes]
rs59053280	0.96[ASN][1000 genomes]
rs59185549	0.84[ASN][1000 genomes]
rs59649940	0.84[ASN][1000 genomes]
rs59947468	0.90[AFR][1000 genomes]
rs60329449	0.93[ASN][1000 genomes]
rs60336356	0.86[ASN][1000 genomes]
rs60719866	0.96[AFR][1000 genomes]
rs60887312	0.83[AFR][1000 genomes]
rs61056382	1.00[ASN][1000 genomes]
rs61094144	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61185790	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61199255	0.84[ASN][1000 genomes]
rs61254540	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6547656	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6547657	1.00[AFR][1000 genomes]
rs6704777	1.00[AFR][1000 genomes]
rs6708146	1.00[AFR][1000 genomes]
rs6712535	1.00[AFR][1000 genomes]
rs6712576	1.00[AFR][1000 genomes]
rs6724612	0.93[AFR][1000 genomes]
rs6737211	1.00[AFR][1000 genomes]
rs6741224	0.91[JPT][hapmap]
rs6741815	1.00[AFR][1000 genomes]
rs6741832	1.00[AFR][1000 genomes]
rs6755224	1.00[AFR][1000 genomes]
rs6755228	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6755246	0.96[AFR][1000 genomes]
rs6760112	1.00[EUR][1000 genomes]
rs7557349	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7569577	1.00[AFR][1000 genomes]
rs7572206	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7582484	1.00[AFR][1000 genomes]
rs7599656	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7606062	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770086	POLR1A	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86267800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:86260800-86268800	Weak transcription	Ovary	ovary
16	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus
18	chr2:86263800-86268000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:86263800-86268800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:86263800-86269200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr2:86264000-86268200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:86264000-86269000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
24	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:86264200-86268400	Enhancers	Primary T cells from cord blood	blood
26	chr2:86264200-86269600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:86264200-86275400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:86264400-86269000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:86264400-86269800	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr2:86264400-86279400	Strong transcription	Hela-S3	cervix
31	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:86264400-86285400	Strong transcription	A549	lung
33	chr2:86264600-86267600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:86264600-86267600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:86264600-86273800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:86264800-86269800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr2:86264800-86273000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:86264800-86275400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:86265000-86268200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
40	chr2:86265000-86269800	Genic enhancers	Fetal Muscle Leg	muscle
41	chr2:86265200-86268800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:86265200-86268800	Genic enhancers	Dnd41	blood
43	chr2:86265200-86281600	Strong transcription	HMEC	breast
44	chr2:86265200-86284000	Strong transcription	NHEK	skin
45	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:86265400-86269000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:86265400-86269200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:86265400-86282600	Strong transcription	Esophagus	oesophagus
49	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
50	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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