Variant report

Variant	rs2686823
Chromosome Location	chr7:47976985-47976986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47976259..47978373-chr7:47980389..47982927,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1056663	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs12702401	0.91[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879833	0.93[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1879834	0.93[CEU][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2037483	0.85[EUR][1000 genomes]
rs2037485	0.85[EUR][1000 genomes]
rs2242477	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2242478	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2242479	0.88[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2686816	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2686817	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686820	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686821	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686825	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686827	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686830	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]
rs2686831	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]
rs2686832	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686833	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2686834	0.85[EUR][1000 genomes]
rs2686835	0.93[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs2686836	0.93[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2686838	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs2686839	0.84[EUR][1000 genomes]
rs2686841	0.83[EUR][1000 genomes]
rs2708853	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708858	0.81[EUR][1000 genomes]
rs2708859	0.81[EUR][1000 genomes]
rs2708861	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2708862	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2708873	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708875	0.81[CEU][hapmap]
rs2708877	0.85[EUR][1000 genomes]
rs2708878	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708880	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708881	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708882	0.85[EUR][1000 genomes]
rs2708894	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]
rs2708895	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708896	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2708897	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708898	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708901	0.80[CEU][hapmap]
rs2708902	0.82[EUR][1000 genomes]
rs2708903	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs2708905	0.89[CEU][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]
rs2708910	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708911	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708913	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3176478	0.87[JPT][hapmap]
rs3176564	0.92[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs34016848	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35536957	0.83[EUR][1000 genomes]
rs4720624	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs57995674	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60107343	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67565252	0.80[ASN][1000 genomes]
rs6955251	0.83[JPT][hapmap]
rs885337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939904	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953572	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9648569	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][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
rs2686823	PKD1L1	cis	parietal	SCAN
rs2686823	ABCA13	cis	parietal	SCAN
rs2686823	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2686823	UPP1	cis	cerebellum	SCAN
rs2686823	HUS1	cis	cerebellum	SCAN
rs2686823	POLM	cis	parietal	SCAN
rs2686823	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
2	chr7:47965800-47980400	Weak transcription	Aorta	Aorta
3	chr7:47967000-47977400	Weak transcription	Right Ventricle	heart
4	chr7:47967600-47993400	Weak transcription	Brain Anterior Caudate	brain
5	chr7:47972400-47977000	Weak transcription	Spleen	Spleen
6	chr7:47972400-47979200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:47972600-47977800	Weak transcription	Fetal Thymus	thymus
8	chr7:47972600-47979000	Weak transcription	Right Atrium	heart
9	chr7:47972600-47980400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:47972800-47979600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:47974000-47977400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:47974000-47979600	Weak transcription	Adipose Nuclei	Adipose
13	chr7:47974400-47977200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr7:47974400-47977600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:47974600-47977600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:47974800-47977000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:47974800-47979400	Weak transcription	Lung	lung
18	chr7:47974800-47979400	Weak transcription	HSMMtube	muscle
19	chr7:47974800-47980200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:47975000-47979000	Weak transcription	Fetal Intestine Small	intestine
21	chr7:47975800-47977200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr7:47975800-47979000	Enhancers	Primary B cells from peripheral blood	blood
23	chr7:47975800-47982400	Enhancers	Fetal Heart	heart
24	chr7:47976000-47977000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:47976000-47977200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr7:47976000-47977200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr7:47976000-47977200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr7:47976000-47979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:47976000-47986000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:47976200-47977200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:47976200-47978600	Enhancers	Primary B cells from cord blood	blood
32	chr7:47976400-47977600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:47976600-47978000	Enhancers	Left Ventricle	heart
34	chr7:47976600-47978200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr7:47976600-47978400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:47976600-47980800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:47976800-47977200	Enhancers	GM12878-XiMat	blood
38	chr7:47976800-47979600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links