Variant report

Variant	rs6871710
Chromosome Location	chr5:58770561-58770562
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10514862	0.85[CHD][hapmap]
rs1120303	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16877169	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16889853	0.92[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs16889865	0.83[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs16889869	0.83[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16889878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16889906	1.00[CHD][hapmap]
rs16889913	1.00[CHB][hapmap]
rs16889921	0.85[CHD][hapmap]
rs17795692	0.86[GIH][hapmap];0.82[TSI][hapmap]
rs17796040	0.86[GIH][hapmap]
rs1824154	0.87[GIH][hapmap]
rs2081092	0.87[GIH][hapmap]
rs28666954	0.94[EUR][1000 genomes]
rs28729916	0.94[EUR][1000 genomes]
rs41447947	0.92[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs56173502	0.96[EUR][1000 genomes]
rs56349317	0.92[EUR][1000 genomes]
rs58232524	0.94[EUR][1000 genomes]
rs59152084	0.94[EUR][1000 genomes]
rs59246284	0.91[EUR][1000 genomes]
rs60509830	0.94[EUR][1000 genomes]
rs6450519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73097336	0.83[ASN][1000 genomes]
rs7704141	0.88[EUR][1000 genomes]
rs7711639	0.82[ASW][hapmap];0.84[LWK][hapmap]
rs7729912	1.00[JPT][hapmap]
rs7737908	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs7738023	0.92[ASN][1000 genomes]
rs9687424	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv881707	chr5:58741491-58784102	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6871710	C5orf35	cis	cerebellum	SCAN
rs6871710	PART1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58754600-58780200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:58756800-58775400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr5:58756800-58775600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:58762000-58778800	Weak transcription	Aorta	Aorta
5	chr5:58762600-58780600	Weak transcription	Fetal Lung	lung
6	chr5:58766000-58774800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:58767200-58771000	Weak transcription	Psoas Muscle	Psoas
8	chr5:58768200-58772200	Weak transcription	Fetal Brain Male	brain
9	chr5:58768800-58779400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:58769000-58770600	Genic enhancers	A549	lung
11	chr5:58769600-58771000	Enhancers	Colon Smooth Muscle	Colon
12	chr5:58770200-58771000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:58770200-58779400	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links