Variant report

Variant	rs10511111
Chromosome Location	chr3:80599757-80599758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1013409	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11127705	0.88[ASN][1000 genomes]
rs11127706	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs11715019	0.88[ASN][1000 genomes]
rs13061012	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2372502	0.90[ASN][1000 genomes]
rs34267339	0.88[ASN][1000 genomes]
rs34370299	0.87[ASN][1000 genomes]
rs35937069	0.89[ASN][1000 genomes]
rs58145326	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59888335	0.88[ASN][1000 genomes]
rs61623958	0.87[ASN][1000 genomes]
rs66826901	0.94[ASN][1000 genomes]
rs67409597	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014658	chr3:80035786-80716259	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv536599	chr3:80035786-80716259	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997720	chr3:80035786-80745662	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1004115	chr3:80349665-81043308	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv536601	chr3:80349665-81043308	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1067580	chr3:80416729-81043307	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv492220	chr3:80416729-81043307	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1000592	chr3:80422155-81044175	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1010176	chr3:80534345-80655360	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv877036	chr3:80548364-80635204	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1002321	chr3:80580862-80606823	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	nsv1012779	chr3:80580862-80613096	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
13	nsv527598	chr3:80585455-81250663	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10511111	SEMA4C	trans	cerebellum	SCAN
rs10511111	ROBO2	cis	cerebellum	SCAN
rs10511111	TXLNA	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:80598200-80599800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:80598400-80605200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:80599400-80599800	Enhancers	Colon Smooth Muscle	Colon
4	chr3:80599400-80606000	Weak transcription	NHEK	skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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