Variant report

Variant	rs2686831
Chromosome Location	chr7:47992986-47992987
allele	C/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	chr7:47991487-47994764	K562	blood:	n/a	n/a
2	POLR2A	chr7:47992439-47993316	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:47992981-47993380	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr7:47992610-47993026	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr7:47992728-47993500	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr7:47992844-47994479	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr7:47992384-47993480	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr7:47992432-47994266	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47987905..47990629-chr7:47991579..47994285,2	K562	blood:
2	chr7:47992039..47994251-chr7:48008798..48010394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225507	TF binding region
PKD1L1	TF binding region
ENSG00000158683	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1056663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12702401	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13309127	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037483	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037485	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242477	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242478	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242479	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686816	0.85[CHB][hapmap]
rs2686817	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2686820	0.86[EUR][1000 genomes]
rs2686821	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes]
rs2686823	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686825	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686827	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2686830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686833	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686834	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686839	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686840	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686841	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686842	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708853	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708858	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708859	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708861	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708865	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708873	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708875	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708877	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708878	0.86[EUR][1000 genomes]
rs2708880	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708881	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708882	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708896	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708897	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708898	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708901	0.81[CEU][hapmap]
rs2708902	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708905	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708910	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708911	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2952720	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3176478	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34016848	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35151200	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35536957	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4720624	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs57995674	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60107343	0.86[EUR][1000 genomes]
rs6944437	0.81[CEU][hapmap]
rs885337	0.92[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs939904	0.93[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs939905	0.93[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs953572	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953594	0.84[ASN][1000 genomes]
rs9648569	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2686831	PKD1L1	cis	cerebellum	SCAN
rs2686831	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2686831	UPP1	cis	cerebellum	SCAN
rs2686831	PKD1L1	cis	parietal	SCAN
rs2686831	HUS1	cis	cerebellum	SCAN
rs2686831	POLM	cis	parietal	SCAN
rs2686831	ABCA13	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
3	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:47978400-47993800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
6	chr7:47980600-47994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:47980800-47993000	Weak transcription	Fetal Stomach	stomach
8	chr7:47981200-47995600	Weak transcription	Aorta	Aorta
9	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:47983600-47993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:47983600-47993800	Weak transcription	Osteobl	bone
15	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr7:47983600-48001000	Weak transcription	NHLF	lung
17	chr7:47983800-47993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:47983800-47993800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:47983800-47995800	Weak transcription	NHDF-Ad	bronchial
20	chr7:47984800-47993800	Weak transcription	Esophagus	oesophagus
21	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
23	chr7:47985200-47995000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:47985200-47995400	Weak transcription	Fetal Heart	heart
25	chr7:47985400-47993800	Weak transcription	Placenta	Placenta
26	chr7:47985400-47995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:47985600-48000600	Weak transcription	Ovary	ovary
28	chr7:47986400-47993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:47986400-47993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:47986400-47993800	Weak transcription	HMEC	breast
31	chr7:47986400-47994200	Weak transcription	Small Intestine	intestine
32	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
33	chr7:47986600-47993600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr7:47986600-47994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:47986800-48001800	Weak transcription	NHEK	skin
36	chr7:47987200-47993200	Weak transcription	Fetal Intestine Small	intestine
37	chr7:47987200-47993800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr7:47987200-47994400	Weak transcription	Right Ventricle	heart
39	chr7:47987800-47994000	Weak transcription	Lung	lung
40	chr7:47988200-47993400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:47988600-47993000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:47988600-47993600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:47988600-47994600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:47988800-47994200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr7:47989600-47993600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:47989800-47993800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:47990000-47993600	Weak transcription	Left Ventricle	heart
48	chr7:47990000-47993800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:47990000-47994000	Weak transcription	Spleen	Spleen
50	chr7:47990000-47995600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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