Variant report

Variant	rs3770084
Chromosome Location	chr2:86279005-86279006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86277732..86280546-chr2:86295705..86298565,2	MCF-7	breast:
2	chr2:86278837..86281699-chr2:86305012..86307406,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10184159	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689889	0.85[CHB][hapmap]
rs12124	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17026904	1.00[ASN][1000 genomes]
rs17579744	0.90[JPT][hapmap]
rs1978842	0.90[JPT][hapmap]
rs2278086	0.87[GIH][hapmap]
rs2278532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278533	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278534	1.00[ASN][1000 genomes]
rs2278535	1.00[ASN][1000 genomes]
rs2278537	0.96[ASN][1000 genomes]
rs2288116	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731815	0.85[GIH][hapmap]
rs3731816	0.85[GIH][hapmap]
rs3731822	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3755005	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770063	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3770064	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3770076	1.00[ASN][1000 genomes]
rs3770083	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770085	1.00[ASN][1000 genomes]
rs3770086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770088	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3770091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821019	1.00[ASN][1000 genomes]
rs56861544	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57150140	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57318396	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57361751	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57405155	0.89[ASN][1000 genomes]
rs57963460	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58002521	0.81[ASN][1000 genomes]
rs58009603	1.00[ASN][1000 genomes]
rs58026145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58429119	1.00[EUR][1000 genomes]
rs58810051	0.87[ASN][1000 genomes]
rs58861315	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58913632	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58919291	1.00[ASN][1000 genomes]
rs59053280	1.00[ASN][1000 genomes]
rs59185549	0.88[ASN][1000 genomes]
rs59649940	0.88[ASN][1000 genomes]
rs60329449	0.96[ASN][1000 genomes]
rs60336356	0.82[ASN][1000 genomes]
rs61056382	0.96[ASN][1000 genomes]
rs61094144	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61185790	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61199255	0.81[ASN][1000 genomes]
rs61254540	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741224	0.90[JPT][hapmap]
rs6755228	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760112	1.00[EUR][1000 genomes]
rs7599656	1.00[TSI][hapmap]

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	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
2	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
3	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
4	nsv522891	chr2:86278992-86281905	Strong transcription Genic enhancers Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770084	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	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr2:86251200-86283000	Strong transcription	HepG2	liver
3	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
11	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:86264400-86279400	Strong transcription	Hela-S3	cervix
13	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:86264400-86285400	Strong transcription	A549	lung
15	chr2:86265200-86281600	Strong transcription	HMEC	breast
16	chr2:86265200-86284000	Strong transcription	NHEK	skin
17	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:86265400-86282600	Strong transcription	Esophagus	oesophagus
19	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
20	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:86265400-86289800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:86265600-86282000	Strong transcription	K562	blood
23	chr2:86265600-86282400	Strong transcription	Brain Germinal Matrix	brain
24	chr2:86265600-86289800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:86265800-86280400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:86265800-86284000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:86266000-86281800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:86266000-86282600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:86266000-86282800	Strong transcription	Gastric	stomach
31	chr2:86266000-86282800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:86266000-86283800	Strong transcription	Fetal Intestine Small	intestine
33	chr2:86266000-86287800	Weak transcription	Right Atrium	heart
34	chr2:86266200-86280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:86266200-86281000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:86266200-86281400	Strong transcription	NHLF	lung
37	chr2:86266200-86281600	Strong transcription	Osteobl	bone
38	chr2:86266200-86282200	Strong transcription	GM12878-XiMat	blood
39	chr2:86266200-86282800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:86266200-86282800	Strong transcription	Fetal Stomach	stomach
41	chr2:86266200-86284600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:86266400-86281400	Strong transcription	Liver	Liver
43	chr2:86266400-86281600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:86266400-86288800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:86266400-86295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:86266600-86285000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:86266800-86289800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:86267000-86281400	Strong transcription	HSMMtube	muscle
49	chr2:86267200-86290800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:86267400-86283200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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