Variant report

Variant	rs10929781
Chromosome Location	chr2:12183955-12183956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10210269	0.82[CHB][hapmap]
rs10929776	0.87[CHB][hapmap]
rs11675063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471493	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12692452	0.80[EUR][1000 genomes]
rs12987412	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002231	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13007105	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1550395	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1550396	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1550398	0.87[CHB][hapmap]
rs2165219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2380405	0.84[ASN][1000 genomes]
rs6432249	0.84[ASN][1000 genomes]
rs6432250	0.84[ASN][1000 genomes]
rs751579	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7560369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7584343	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584367	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585074	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10929781	C2orf50	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12181400-12185000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr2:12181600-12193200	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:12182000-12184600	Enhancers	Primary B cells from cord blood	blood
4	chr2:12182200-12185000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr2:12182400-12184800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:12182600-12189200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:12182600-12189400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:12182800-12184000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:12183000-12184400	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:12183200-12186800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:12183400-12184000	Weak transcription	K562	blood
12	chr2:12183400-12184600	Enhancers	GM12878-XiMat	blood
13	chr2:12183400-12185200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:12183600-12184000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:12183600-12184200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:12183600-12184600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:12183600-12185000	Enhancers	Primary T cells from cord blood	blood
18	chr2:12183600-12187000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:12183600-12189400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr2:12183800-12185000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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