Variant report

Variant	rs3731815
Chromosome Location	chr2:86444518-86444519
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86443636..86445724-chr2:86466599..86469156,2	K562	blood:
2	chr2:86398700..86401463-chr2:86444165..86446828,2	K562	blood:
3	chr2:86442543..86445065-chr2:86669308..86671294,2	K562	blood:
4	chr2:86430476..86432923-chr2:86442566..86444856,2	MCF-7	breast:
5	chr2:86420399..86424157-chr2:86440260..86444660,8	K562	blood:
6	chr2:86442147..86446195-chr2:86448137..86451123,4	K562	blood:

Variant related genes	Relation type
ENSG00000273080	Chromatin interaction
ENSG00000115548	Chromatin interaction
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11127018	0.82[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1863062	0.90[JPT][hapmap]
rs3731816	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731817	1.00[CHB][hapmap]
rs3731822	0.85[GIH][hapmap]
rs3770063	0.82[JPT][hapmap]
rs3770064	1.00[GIH][hapmap];0.82[JPT][hapmap]
rs3821015	0.90[JPT][hapmap]
rs3827551	0.85[GIH][hapmap]
rs6716825	0.90[JPT][hapmap]
rs6728494	0.90[JPT][hapmap]
rs6760222	0.90[JPT][hapmap]
rs73946352	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593666	0.90[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3731815	POLR1A	cis	multi-tissue	Pritchard
rs3731815	POLR1A	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86427200-86450200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86427400-86448200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:86429600-86448200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:86438600-86452200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:86439000-86450000	Weak transcription	Fetal Kidney	kidney
6	chr2:86439200-86448400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:86439600-86448600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:86439600-86449800	Weak transcription	Small Intestine	intestine
9	chr2:86439600-86450600	Weak transcription	Fetal Brain Male	brain
10	chr2:86439800-86444600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:86439800-86448200	Weak transcription	Lung	lung
12	chr2:86439800-86449400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:86439800-86449600	Weak transcription	Brain Substantia Nigra	brain
14	chr2:86439800-86449800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:86439800-86450000	Weak transcription	Pancreas	Pancrea
16	chr2:86439800-86450000	Weak transcription	Spleen	Spleen
17	chr2:86439800-86450400	Weak transcription	HMEC	breast
18	chr2:86439800-86450600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:86439800-86452200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:86439800-86452200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:86440000-86448200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:86440000-86450000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:86440000-86450200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:86440000-86451200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:86440000-86452200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:86440000-86452800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:86440200-86445600	Weak transcription	Fetal Stomach	stomach
28	chr2:86440200-86448200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:86440200-86450000	Weak transcription	Esophagus	oesophagus
30	chr2:86440200-86450600	Weak transcription	Aorta	Aorta
31	chr2:86440400-86448400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:86440800-86449000	Weak transcription	Right Ventricle	heart
33	chr2:86440800-86451400	Weak transcription	Placenta	Placenta
34	chr2:86441200-86450000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:86441200-86450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:86441200-86450200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:86441400-86448600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:86441400-86450000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:86441400-86450200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:86441600-86445200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:86441600-86445400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:86441600-86445800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:86441600-86446600	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:86441600-86448400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:86441600-86450000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:86441600-86450000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:86441600-86450000	Weak transcription	GM12878-XiMat	blood
48	chr2:86441600-86450200	Weak transcription	Psoas Muscle	Psoas
49	chr2:86441600-86452000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:86441600-86452600	Weak transcription	Thymus	Thymus

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