Variant report

Variant	rs2708895
Chromosome Location	chr7:47993869-47993870
allele	A/G
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	NFATC1	chr7:47993476-47994594	GM12878	blood:	n/a	n/a
3	ATF2	chr7:47993487-47993874	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:47993626-47994102	GM12891	blood:	n/a	n/a
5	POLR2A	chr7:47993659-47994347	GM12892	blood:	n/a	n/a
6	POLR2A	chr7:47993857-47994180	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:47993854-47994241	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXM1	chr7:47993359-47994598	GM12878	blood:	n/a	n/a
9	CREB1	chr7:47993580-47994003	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:47993683-47994206	GM12892	blood:	n/a	n/a
11	POLR2A	chr7:47993602-47993881	K562	blood:	n/a	n/a
12	POLR2A	chr7:47993575-47994028	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr7:47993357-47994086	GM12878	blood:	n/a	n/a
14	MTA3	chr7:47993304-47994761	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:47992844-47994479	Hela-S3	cervix:	n/a	n/a
16	ATF2	chr7:47993317-47994536	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:47993639-47994212	GM12891	blood:	n/a	n/a
18	CEBPB	chr7:47993147-47994623	GM12878	blood:	n/a	chr7:47993883-47993895
19	PML	chr7:47993145-47994614	GM12878	blood:	n/a	n/a
20	RUNX3	chr7:47993474-47993944	GM12878	blood:	n/a	n/a
21	CREB1	chr7:47993396-47994588	GM12878	blood:	n/a	n/a
22	NFATC1	chr7:47993384-47994522	GM12878	blood:	n/a	n/a
23	JUND	chr7:47993591-47993899	K562	blood:	n/a	chr7:47993727-47993736
24	POLR2A	chr7:47993356-47993878	MCF10A-Er-Src	breast:	n/a	n/a
25	NFIC	chr7:47993146-47994680	GM12878	blood:	n/a	chr7:47994304-47994320 chr7:47994303-47994320
26	POLR2A	chr7:47993729-47994073	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr7:47992432-47994266	PANC-1	pancreas:	n/a	n/a
28	RUNX3	chr7:47993223-47994704	GM12878	blood:	n/a	n/a
29	MTA3	chr7:47993224-47994532	GM12878	blood:	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
ENSG00000158683	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

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];0.98[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];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13309127	0.95[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037483	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037485	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242477	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242478	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[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];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686816	0.84[CHB][hapmap]
rs2686817	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs2686820	0.86[EUR][1000 genomes]
rs2686821	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2686823	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686825	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686827	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2686830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686831	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]
rs2686832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686834	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686839	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686840	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2686841	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686842	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708853	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708858	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708859	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708861	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708865	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708873	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708875	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708877	0.92[AFR][1000 genomes];0.98[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708896	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708897	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708901	0.80[CEU][hapmap]
rs2708902	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708905	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[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	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2952720	0.95[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];0.88[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];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34016848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35151200	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35536957	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4720624	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs57995674	0.86[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];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs939904	0.92[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs939905	0.93[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs953572	0.96[CEU][hapmap];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2708895	UPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr7:47977400-48000600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:47978400-47994000	Weak transcription	Fetal Thymus	thymus
4	chr7:47980600-47994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:47981200-47995600	Weak transcription	Aorta	Aorta
6	chr7:47982000-47994000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:47982000-47994000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr7:47982000-47994200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr7:47982000-47999400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:47983600-47994400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:47983600-48001000	Weak transcription	NHLF	lung
12	chr7:47983800-47995800	Weak transcription	NHDF-Ad	bronchial
13	chr7:47984800-47996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:47985000-48001400	Weak transcription	Hela-S3	cervix
15	chr7:47985200-47995000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:47985200-47995400	Weak transcription	Fetal Heart	heart
17	chr7:47985400-47995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:47985600-48000600	Weak transcription	Ovary	ovary
19	chr7:47986400-47994200	Weak transcription	Small Intestine	intestine
20	chr7:47986400-48003800	Weak transcription	Fetal Brain Male	brain
21	chr7:47986600-47994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:47986800-48001800	Weak transcription	NHEK	skin
23	chr7:47987200-47994400	Weak transcription	Right Ventricle	heart
24	chr7:47987800-47994000	Weak transcription	Lung	lung
25	chr7:47988600-47994600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:47988800-47994200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:47990000-47994000	Weak transcription	Spleen	Spleen
28	chr7:47990000-47995600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:47990000-48000600	Weak transcription	Brain Angular Gyrus	brain
30	chr7:47990600-47994000	Weak transcription	Gastric	stomach
31	chr7:47990600-47995600	Weak transcription	Brain Substantia Nigra	brain
32	chr7:47990600-47995800	Weak transcription	Right Atrium	heart
33	chr7:47990600-48000600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:47991000-47994200	Weak transcription	Fetal Intestine Large	intestine
35	chr7:47991000-48001400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:47991400-48001000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr7:47991400-48003600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr7:47991400-48004800	Weak transcription	Fetal Kidney	kidney
39	chr7:47991600-47994400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:47991600-48000600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:47991600-48000600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:47991800-47994200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:47992000-47994000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:47992000-47994000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:47992000-47995400	Weak transcription	K562	blood
46	chr7:47992000-48000400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:47992000-48000600	Weak transcription	Brain Germinal Matrix	brain
48	chr7:47992000-48001600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr7:47992000-48001600	Weak transcription	Pancreas	Pancrea
50	chr7:47992000-48002400	Weak transcription	HepG2	liver

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