Variant report

Variant	rs17616899
Chromosome Location	chr7:12785780-12785781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:12728909..12731157-chr7:12785382..12787852,3	K562	blood:
2	chr7:12768764..12771206-chr7:12785480..12787516,3	K562	blood:
3	chr7:12778078..12781054-chr7:12784159..12786247,3	K562	blood:
4	chr7:12726393..12728839-chr7:12782362..12787533,4	K562	blood:
5	chr7:12773603..12776314-chr7:12785559..12788472,3	K562	blood:
6	chr7:12768573..12770264-chr7:12785480..12787749,2	K562	blood:

Variant related genes	Relation type
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11971985	0.82[AFR][1000 genomes]
rs11974943	0.94[LWK][hapmap];0.98[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs11977551	0.87[AFR][1000 genomes]
rs11978862	0.87[AFR][1000 genomes]
rs11981713	0.86[AFR][1000 genomes]
rs1524937	0.94[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs2058047	0.82[AFR][1000 genomes]
rs2058048	0.85[AFR][1000 genomes]
rs34655971	0.87[AFR][1000 genomes]
rs4719329	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs55694038	0.87[AFR][1000 genomes]
rs56083439	0.80[AFR][1000 genomes]
rs57829157	0.81[AFR][1000 genomes]
rs6954577	0.86[AFR][1000 genomes]
rs6961321	0.87[AFR][1000 genomes]
rs73055478	0.85[AFR][1000 genomes]
rs73055481	0.82[AFR][1000 genomes]
rs73055489	0.85[AFR][1000 genomes]
rs73055490	0.82[AFR][1000 genomes]
rs73061017	0.87[AFR][1000 genomes]
rs73061027	0.87[AFR][1000 genomes]
rs7784389	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	esv2422346	chr7:12739291-12883550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1027501	chr7:12743592-12927109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2763623	chr7:12777205-12813460	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv464380	chr7:12777308-12805000	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv606233	chr7:12777308-12805000	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv464381	chr7:12777308-12826398	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv470077	chr7:12777308-12826398	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv606234	chr7:12777308-12826398	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17616899	NXPH1	cis	parietal	SCAN
rs17616899	SCIN	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12771200-12789400	Weak transcription	Psoas Muscle	Psoas
2	chr7:12782200-12787600	Weak transcription	HMEC	breast
3	chr7:12785200-12786200	Enhancers	HUVEC	blood vessel
4	chr7:12785400-12787000	Weak transcription	K562	blood
5	chr7:12785600-12786000	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links