Variant report

Variant	rs2708861
Chromosome Location	chr7:48016717-48016718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48015837..48017649-chr7:48045568..48048031,2	K562	blood:
2	chr7:48014982..48017328-chr7:48026575..48029341,3	K562	blood:
3	chr7:48016563..48017117-chr7:48149518..48150034,2	MCF-7	breast:
4	chr7:48012956..48017232-chr7:48017620..48020627,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164744	Chromatin interaction
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1056663	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702401	0.95[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13309127	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879834	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[MKK][hapmap];1.00[TSI][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]
rs2037483	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037485	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242477	1.00[ASW][hapmap];1.00[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];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242478	0.88[ASW][hapmap];1.00[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242479	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686816	0.85[CHB][hapmap]
rs2686817	0.87[JPT][hapmap]
rs2686820	0.81[EUR][1000 genomes]
rs2686821	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2686823	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2686825	0.81[EUR][1000 genomes]
rs2686830	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];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686831	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]
rs2686832	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]
rs2686833	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686834	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686835	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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686836	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686838	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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686839	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686840	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2686841	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686842	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708853	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708859	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708865	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2708873	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708875	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2708877	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708878	0.81[EUR][1000 genomes]
rs2708880	0.81[EUR][1000 genomes]
rs2708881	0.81[EUR][1000 genomes]
rs2708882	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708894	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];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708895	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]
rs2708896	0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2708897	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708898	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708902	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708903	1.00[ASW][hapmap];0.96[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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708905	1.00[ASW][hapmap];1.00[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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708910	0.81[EUR][1000 genomes]
rs2708911	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2952720	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3176478	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3176564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34016848	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35151200	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35536957	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4720624	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs57995674	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60107343	0.81[EUR][1000 genomes]
rs885337	0.88[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs939904	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs939905	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs953572	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953594	0.88[ASN][1000 genomes]
rs9648569	0.81[CEU][hapmap];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
rs2708861	PKD1L1	cis	parietal	SCAN
rs2708861	UPP1	cis	cerebellum	SCAN
rs2708861	POLM	cis	parietal	SCAN
rs2708861	PKD1L1	cis	cerebellum	SCAN
rs2708861	ABCA13	cis	parietal	SCAN
rs2708861	HUS1	cis	cerebellum	SCAN
rs2708861	UPP1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47999600-48017600	Strong transcription	Primary T cells from cord blood	blood
2	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
3	chr7:48000200-48017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:48000400-48016800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:48000400-48017600	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr7:48000400-48017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:48000400-48017600	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:48000400-48017800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr7:48000400-48017800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:48000600-48017600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:48001600-48017600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:48002000-48018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:48007400-48018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:48009200-48016800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr7:48009600-48018000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:48009800-48018000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:48010000-48018000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr7:48010200-48017600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:48010200-48017800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:48010200-48017800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:48010200-48018200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:48010400-48017600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr7:48010400-48018000	Strong transcription	Fetal Muscle Leg	muscle
24	chr7:48010400-48018200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:48010600-48017800	Strong transcription	Brain Anterior Caudate	brain
26	chr7:48010600-48018000	Strong transcription	Primary B cells from cord blood	blood
27	chr7:48010600-48018000	Strong transcription	Fetal Lung	lung
28	chr7:48010800-48016800	Strong transcription	Adipose Nuclei	Adipose
29	chr7:48010800-48017200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:48010800-48017600	Strong transcription	Hela-S3	cervix
31	chr7:48010800-48018000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr7:48010800-48018000	Strong transcription	Placenta	Placenta
33	chr7:48010800-48018000	Strong transcription	Fetal Stomach	stomach
34	chr7:48010800-48018000	Strong transcription	Spleen	Spleen
35	chr7:48011000-48017200	Strong transcription	Brain Germinal Matrix	brain
36	chr7:48011000-48017400	Strong transcription	Lung	lung
37	chr7:48011000-48017600	Strong transcription	HSMMtube	muscle
38	chr7:48011000-48017800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:48011000-48017800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:48011000-48018000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:48011000-48018200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr7:48011200-48017200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr7:48011200-48017600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:48011200-48017800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:48011200-48017800	Strong transcription	Brain Angular Gyrus	brain
46	chr7:48011200-48017800	Strong transcription	NH-A	brain
47	chr7:48011200-48018000	Weak transcription	Right Atrium	heart
48	chr7:48011200-48018200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:48011400-48017600	Strong transcription	Osteobl	bone
50	chr7:48011400-48017800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links