Variant report

Variant	rs2708659
Chromosome Location	chr7:12658980-12658981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12654024..12655962-chr7:12657053..12659139,2	K562	blood:
2	chr7:12656084..12659203-chr7:12659962..12662928,5	K562	blood:

Variant related genes	Relation type
ENSG00000006747	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10241553	0.85[CHB][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10258985	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs10268615	0.90[CEU][hapmap];0.83[CHB][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12537710	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs1404519	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2041117	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs2056621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2074866	0.81[GIH][hapmap]
rs2190716	0.98[ASN][1000 genomes]
rs2529784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2529786	0.84[GIH][hapmap]
rs2691817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691819	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.99[ASN][1000 genomes]
rs2691820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2691822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691823	0.94[CHB][hapmap];0.80[JPT][hapmap];0.98[ASN][1000 genomes]
rs2708658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2708660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34199326	0.85[EUR][1000 genomes]
rs702477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs849758	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs849801	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2708659	NXPH1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12625400-12667600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:12650000-12660200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:12652800-12659400	Weak transcription	K562	blood
4	chr7:12657200-12659600	Enhancers	Stomach Mucosa	stomach
5	chr7:12657800-12659400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:12658000-12661200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:12658400-12659000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr7:12658400-12661600	Enhancers	HUVEC	blood vessel
9	chr7:12658600-12659600	Enhancers	A549	lung
10	chr7:12658800-12665600	Weak transcription	Placenta	Placenta

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