Variant report

Variant	rs10085602
Chromosome Location	chr7:3633017-3633018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10231366	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10236517	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10238783	0.81[CEU][hapmap]
rs10247668	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10256371	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs10259072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260149	1.00[ASN][1000 genomes]
rs10275747	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499336	0.82[MEX][hapmap]
rs11972207	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11976762	1.00[ASN][1000 genomes]
rs11977942	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17133439	0.86[CEU][hapmap]
rs17133471	1.00[CHB][hapmap]
rs2141820	1.00[CHB][hapmap]
rs56025717	1.00[ASN][1000 genomes]
rs6462121	0.81[CEU][hapmap]
rs6943054	1.00[ASN][1000 genomes]
rs73037685	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039639	1.00[ASN][1000 genomes]
rs7776767	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7792749	1.00[ASN][1000 genomes]
rs7793515	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7793775	1.00[ASN][1000 genomes]
rs7795323	0.82[CEU][hapmap]
rs7800962	0.81[CEU][hapmap]
rs957360	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv887334	chr7:3531275-3635105	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1023888	chr7:3539750-3638242	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1034298	chr7:3539750-3646251	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1792280	chr7:3592290-3668229	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1017012	chr7:3602397-3638242	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv538679	chr7:3602397-3638242	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv605909	chr7:3605340-3638547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv948390	chr7:3609821-3734421	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1033415	chr7:3616095-3753563	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv538680	chr7:3616095-3753563	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1016930	chr7:3627295-3705057	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv530553	chr7:3629504-3736851	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10085602	SLC29A4	cis	cerebellum	SCAN
rs10085602	SDK1	cis	parietal	SCAN
rs10085602	NENF	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3630400-3633400	Enhancers	H1 Cell Line	embryonic stem cell
2	chr7:3630800-3633200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:3630800-3633400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:3630800-3633400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:3631000-3633200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:3631200-3636000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:3632200-3633400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:3632200-3633400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:3632400-3634600	Weak transcription	Fetal Brain Male	brain
10	chr7:3632600-3633200	Enhancers	Duodenum Mucosa	Duodenum
11	chr7:3632600-3633400	Enhancers	Pancreas	Pancrea
12	chr7:3632600-3638000	Weak transcription	Fetal Brain Female	brain
13	chr7:3632800-3633200	Enhancers	Stomach Mucosa	stomach
14	chr7:3633000-3635000	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links