Variant report

Variant	rs3770088
Chromosome Location	chr2:86263941-86263942
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10184159	0.84[ASN][1000 genomes]
rs11689889	0.86[CHB][hapmap]
rs12124	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17026904	0.84[ASN][1000 genomes]
rs17579744	0.82[JPT][hapmap]
rs1978842	0.81[JPT][hapmap]
rs2278532	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2278533	0.84[ASN][1000 genomes]
rs2278534	0.84[ASN][1000 genomes]
rs2278535	0.84[ASN][1000 genomes]
rs2278537	0.87[ASN][1000 genomes]
rs2288116	0.84[ASN][1000 genomes]
rs3731822	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3755005	0.87[ASN][1000 genomes]
rs3770063	1.00[CHB][hapmap]
rs3770064	1.00[CHB][hapmap]
rs3770076	0.84[ASN][1000 genomes]
rs3770083	0.84[ASN][1000 genomes]
rs3770084	0.84[ASN][1000 genomes]
rs3770085	0.84[ASN][1000 genomes]
rs3770086	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3770091	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3821019	0.84[ASN][1000 genomes]
rs57150140	0.84[ASN][1000 genomes]
rs58009603	0.84[ASN][1000 genomes]
rs58026145	0.84[ASN][1000 genomes]
rs58810051	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58861315	0.84[ASN][1000 genomes]
rs58919291	0.84[ASN][1000 genomes]
rs59053280	0.84[ASN][1000 genomes]
rs59757945	1.00[EUR][1000 genomes]
rs60313984	1.00[EUR][1000 genomes]
rs60329449	0.80[ASN][1000 genomes]
rs61028280	1.00[EUR][1000 genomes]
rs61056382	0.87[ASN][1000 genomes]
rs61185790	0.84[ASN][1000 genomes]
rs61254540	0.84[ASN][1000 genomes]
rs6741224	0.82[JPT][hapmap]
rs6755228	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770088	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	chr2:86257200-86264400	Strong transcription	K562	blood
14	chr2:86258200-86265400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:86260200-86266200	Genic enhancers	Fetal Stomach	stomach
16	chr2:86260600-86265000	Enhancers	Fetal Heart	heart
17	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:86260800-86264200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:86260800-86268800	Weak transcription	Ovary	ovary
21	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:86261400-86265600	Enhancers	Left Ventricle	heart
23	chr2:86261400-86266200	Enhancers	Psoas Muscle	Psoas
24	chr2:86261600-86265600	Enhancers	Right Ventricle	heart
25	chr2:86261800-86266400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:86262000-86265800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:86262200-86264400	Enhancers	Liver	Liver
28	chr2:86262400-86264000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:86262400-86264200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr2:86262400-86264200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:86262400-86264400	Enhancers	Brain Anterior Caudate	brain
32	chr2:86262400-86265200	Enhancers	Spleen	Spleen
33	chr2:86262400-86265200	Genic enhancers	NHEK	skin
34	chr2:86262400-86266000	Genic enhancers	Brain Angular Gyrus	brain
35	chr2:86262400-86266000	Genic enhancers	Fetal Intestine Small	intestine
36	chr2:86262400-86266000	Enhancers	Right Atrium	heart
37	chr2:86262400-86266200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:86262400-86266200	Enhancers	Lung	lung
39	chr2:86262400-86266800	Genic enhancers	Placenta	Placenta
40	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus
41	chr2:86262600-86264200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:86262600-86264200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:86262600-86264400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr2:86262600-86264400	Weak transcription	Hela-S3	cervix
45	chr2:86262600-86264600	Enhancers	Brain Hippocampus Middle	brain
46	chr2:86262600-86264800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:86262600-86264800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:86262600-86265200	Enhancers	Fetal Kidney	kidney
49	chr2:86262600-86265600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:86262600-86265600	Genic enhancers	Brain Germinal Matrix	brain

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