Variant report

Variant	rs2065465
Chromosome Location	chr10:45416256-45416257
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASSF4-2	chr10:45415873-45416730	NONHSAT013045

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10793566	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10793567	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10793568	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10793569	0.89[JPT][hapmap]
rs10900131	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11239278	1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1332622	1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4543933	1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4948929	0.87[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs4948931	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs6593448	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs6593449	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7077388	1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs7082940	0.97[EUR][1000 genomes]
rs7085840	1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7095112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7098274	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7100544	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7911339	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7923073	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7923091	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs932986	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][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	nsv517161	chr10:45210690-45416256	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv466909	chr10:45408011-45446791	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550714	chr10:45408011-45446791	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2065465	ZNF488	cis	parietal	SCAN
rs2065465	RASGEF1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45406400-45419000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:45407800-45422800	Weak transcription	Ovary	ovary
3	chr10:45408600-45417200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:45410000-45419000	Weak transcription	Pancreas	Pancrea
5	chr10:45410200-45430400	Weak transcription	Gastric	stomach
6	chr10:45410600-45419600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:45413200-45420400	Weak transcription	Fetal Kidney	kidney
8	chr10:45413400-45428200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr10:45413800-45416400	Weak transcription	Brain Angular Gyrus	brain
10	chr10:45413800-45417000	Weak transcription	Fetal Intestine Small	intestine
11	chr10:45415400-45420000	Weak transcription	HSMMtube	muscle
12	chr10:45415600-45417000	Strong transcription	Fetal Brain Female	brain
13	chr10:45416200-45416400	Weak transcription	Fetal Stomach	stomach
14	chr10:45416200-45419800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links