Variant report

Variant	rs3770063
Chromosome Location	chr2:86403499-86403500
allele	A/T
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	chr2:86403368-86403542	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86397231..86400084-chr2:86401691..86405025,4	K562	blood:

Variant related genes	Relation type
IMMT	TF binding region
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10184159	0.88[ASN][1000 genomes]
rs12124	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17026904	0.88[ASN][1000 genomes]
rs2241434	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2278532	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2278533	0.88[ASN][1000 genomes]
rs2278534	0.88[ASN][1000 genomes]
rs2278535	0.88[ASN][1000 genomes]
rs2278537	0.84[ASN][1000 genomes]
rs2288116	0.88[ASN][1000 genomes]
rs3731815	0.82[JPT][hapmap]
rs3731816	0.82[JPT][hapmap]
rs3731822	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs3755005	0.84[ASN][1000 genomes]
rs3764948	0.91[EUR][1000 genomes]
rs3770064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3770076	0.88[ASN][1000 genomes]
rs3770083	0.88[ASN][1000 genomes]
rs3770084	0.88[ASN][1000 genomes]
rs3770085	0.88[ASN][1000 genomes]
rs3770086	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3770088	1.00[CHB][hapmap]
rs3770091	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3821019	0.88[ASN][1000 genomes]
rs41291149	1.00[AMR][1000 genomes]
rs57150140	0.88[ASN][1000 genomes]
rs58002521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58009603	0.88[ASN][1000 genomes]
rs58026145	0.88[ASN][1000 genomes]
rs58678485	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58861315	0.88[ASN][1000 genomes]
rs58919291	0.88[ASN][1000 genomes]
rs59053280	0.88[ASN][1000 genomes]
rs59185549	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59649940	1.00[ASN][1000 genomes]
rs60329449	0.84[ASN][1000 genomes]
rs61056382	0.84[ASN][1000 genomes]
rs61185790	0.88[ASN][1000 genomes]
rs61254540	0.88[ASN][1000 genomes]
rs6755228	0.88[ASN][1000 genomes]
rs7562837	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats 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	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer 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	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS 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
6	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS 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
7	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS 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
8	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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
9	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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
10	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS 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
12	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS 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
13	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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
14	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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
15	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats 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
17	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv458574	chr2:86385728-86507688	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv582372	chr2:86385728-86507688	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3770063	POLR1A	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86335000-86409000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86335400-86408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:86335600-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:86335600-86408600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:86336800-86407400	Strong transcription	Dnd41	blood
6	chr2:86342800-86408600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:86342800-86408600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:86343000-86408600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:86379800-86407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:86381600-86409000	Strong transcription	Fetal Thymus	thymus
11	chr2:86381800-86407400	Strong transcription	Liver	Liver
12	chr2:86381800-86409000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:86386200-86413000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:86387600-86410000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:86390000-86407600	Strong transcription	A549	lung
16	chr2:86390400-86421200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:86390600-86404800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:86390600-86411200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:86393400-86413400	Weak transcription	Gastric	stomach
20	chr2:86393800-86405000	Weak transcription	Pancreas	Pancrea
21	chr2:86393800-86405600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:86393800-86406400	Weak transcription	Spleen	Spleen
23	chr2:86393800-86413600	Weak transcription	Esophagus	oesophagus
24	chr2:86394800-86407000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:86394800-86407400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:86394800-86408600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:86394800-86409000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:86395200-86405000	Strong transcription	K562	blood
29	chr2:86395200-86408600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:86395400-86407200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:86396000-86408000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:86396400-86412600	Weak transcription	Brain Anterior Caudate	brain
33	chr2:86396600-86413000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:86397200-86407200	Strong transcription	Fetal Brain Female	brain
35	chr2:86398000-86406200	Weak transcription	Fetal Kidney	kidney
36	chr2:86398400-86406600	Weak transcription	Small Intestine	intestine
37	chr2:86398600-86406200	Weak transcription	HUVEC	blood vessel
38	chr2:86398600-86417200	Weak transcription	Fetal Brain Male	brain
39	chr2:86398800-86403600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:86399000-86404000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:86399000-86406200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:86399600-86405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:86399800-86406400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:86400000-86404200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:86400000-86404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:86400000-86405000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:86400000-86405000	Weak transcription	Colonic Mucosa	Colon
48	chr2:86400000-86405200	Weak transcription	Lung	lung
49	chr2:86400000-86406200	Weak transcription	NHLF	lung
50	chr2:86400000-86411400	Weak transcription	Aorta	Aorta

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