Variant report

Variant	rs3731822
Chromosome Location	chr2:86248494-86248495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86246321..86249614-chr2:86252792..86256934,5	K562	blood:
2	chr2:86245953..86248682-chr2:86248829..86250857,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLR1A-3	chr2:86248013-86250635	NONHSAT072082
2	lnc-POLR1A-3	chr2:86247339-86250991	NONHSAT072081

Variant related genes	Relation type
ENSG00000068654	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10168997	0.81[ASN][1000 genomes]
rs10184159	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11689889	0.86[CHB][hapmap]
rs12124	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1469981	0.83[ASN][1000 genomes]
rs17026904	0.89[ASN][1000 genomes]
rs17579744	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1978842	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2278086	1.00[ASW][hapmap];0.87[GIH][hapmap]
rs2278532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278533	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278534	0.89[ASN][1000 genomes]
rs2278535	0.89[ASN][1000 genomes]
rs2278537	0.93[ASN][1000 genomes]
rs2288116	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731815	0.85[GIH][hapmap]
rs3731816	0.85[GIH][hapmap]
rs3755005	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770063	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3770064	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs3770076	0.89[ASN][1000 genomes]
rs3770083	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770084	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770085	0.89[ASN][1000 genomes]
rs3770086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770088	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3770091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821019	0.89[ASN][1000 genomes]
rs56861544	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57150140	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57318396	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57361751	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57405155	1.00[ASN][1000 genomes]
rs57963460	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58009603	0.89[ASN][1000 genomes]
rs58026145	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58429119	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58861315	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58913632	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58919291	0.89[ASN][1000 genomes]
rs59053280	0.89[ASN][1000 genomes]
rs60329449	0.86[ASN][1000 genomes]
rs60336356	0.93[ASN][1000 genomes]
rs60471596	0.80[ASN][1000 genomes]
rs60479377	0.88[AFR][1000 genomes]
rs61056382	0.93[ASN][1000 genomes]
rs61094144	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61185790	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61199255	0.91[ASN][1000 genomes]
rs61254540	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6708805	0.83[ASN][1000 genomes]
rs6741224	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6755228	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6760112	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72847838	0.81[ASN][1000 genomes]
rs7572206	1.00[ASW][hapmap]
rs7599656	1.00[ASW][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3731822	POLR1A	cis	lymphoblastoid	seeQTL
rs3731822	POLR1A	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86242200-86251200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86244000-86251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:86244200-86248600	Weak transcription	Right Atrium	heart
4	chr2:86244200-86257000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:86244400-86252400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:86244400-86252600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:86244400-86252800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:86244400-86253000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:86244400-86255000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:86244600-86251000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:86244600-86251200	Weak transcription	Primary T cells from cord blood	blood
12	chr2:86244600-86251400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:86244600-86251400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:86244600-86251800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:86244600-86252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:86244600-86252600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:86244600-86255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:86244600-86257200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:86244800-86253600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:86245000-86251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:86245000-86252400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:86245000-86252600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:86245400-86251000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:86245400-86251200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:86245400-86251200	Weak transcription	A549	lung
26	chr2:86245400-86252400	Weak transcription	Esophagus	oesophagus
27	chr2:86245400-86252600	Weak transcription	Hela-S3	cervix
28	chr2:86245400-86254000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:86245400-86254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:86245400-86257200	Weak transcription	Stomach Mucosa	stomach
31	chr2:86245400-86257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:86245400-86263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:86245600-86251600	Weak transcription	HMEC	breast
34	chr2:86245600-86252400	Weak transcription	NHEK	skin
35	chr2:86245600-86253600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:86245800-86251200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:86245800-86251400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:86246000-86251400	Weak transcription	K562	blood
39	chr2:86246200-86250800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:86246200-86252600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:86246200-86252600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:86246400-86249600	Weak transcription	Primary B cells from cord blood	blood
43	chr2:86246400-86249600	Weak transcription	Thymus	Thymus
44	chr2:86246400-86250000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:86246400-86252600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:86246600-86249600	Weak transcription	GM12878-XiMat	blood
47	chr2:86247000-86249200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:86247000-86251200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:86247400-86249600	Enhancers	Brain Angular Gyrus	brain
50	chr2:86247400-86251000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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