Variant report

Variant	rs3755005
Chromosome Location	chr2:86261514-86261515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

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]
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[ASN][1000 genomes]
rs2288116	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731822	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[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]
rs3770086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821019	0.96[ASN][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]
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]
rs58429119	1.00[EUR][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]
rs60329449	0.93[ASN][1000 genomes]
rs60336356	0.86[ASN][1000 genomes]
rs61056382	1.00[ASN][1000 genomes]
rs61094144	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61185790	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]
rs6741224	0.91[JPT][hapmap]
rs6755228	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760112	1.00[EUR][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
rs3755005	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	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86250800-86262200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:86251000-86262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:86251000-86262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:86251000-86262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:86251200-86261600	Strong transcription	NH-A	brain
7	chr2:86251200-86261800	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:86251200-86262400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:86251200-86262800	Strong transcription	Fetal Brain Female	brain
10	chr2:86251200-86263200	Strong transcription	A549	lung
11	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr2:86251200-86283000	Strong transcription	HepG2	liver
14	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:86251400-86262000	Strong transcription	Osteobl	bone
18	chr2:86251400-86262800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:86251400-86263400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:86251600-86261600	Strong transcription	HMEC	breast
21	chr2:86251800-86262000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:86251800-86262400	Strong transcription	Fetal Intestine Small	intestine
23	chr2:86252000-86262000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:86252200-86262000	Strong transcription	GM12878-XiMat	blood
26	chr2:86252200-86262400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:86252200-86262600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:86252400-86261600	Strong transcription	Esophagus	oesophagus
31	chr2:86252400-86262200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:86252400-86262400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:86252400-86262400	Strong transcription	NHEK	skin
34	chr2:86252400-86262600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr2:86252400-86263000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr2:86252600-86261600	Strong transcription	Pancreas	Pancrea
38	chr2:86252600-86262600	Strong transcription	Hela-S3	cervix
39	chr2:86252600-86262800	Strong transcription	Fetal Intestine Large	intestine
40	chr2:86252600-86263200	Strong transcription	Aorta	Aorta
41	chr2:86252600-86267800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:86252800-86261600	Strong transcription	Gastric	stomach
44	chr2:86252800-86262400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr2:86253000-86262600	Strong transcription	Brain Germinal Matrix	brain
46	chr2:86253000-86262600	Strong transcription	Fetal Lung	lung
47	chr2:86253200-86262800	Weak transcription	Fetal Brain Male	brain
48	chr2:86253600-86261600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:86253800-86262400	Strong transcription	Brain Angular Gyrus	brain
50	chr2:86254200-86261800	Strong transcription	Rectal Smooth Muscle	rectum

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