Variant report

Variant	rs11976237
Chromosome Location	chr7:102641383-102641384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102635238..102638493-chr7:102639697..102643321,6	K562	blood:
2	chr7:102640940..102642955-chr7:102645628..102648374,3	K562	blood:
3	chr7:102636271..102640995-chr7:102641350..102643321,4	K562	blood:
4	chr7:102640940..102644654-chr7:102645333..102648344,5	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10241865	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs10242028	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10271184	0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs10273725	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs10279449	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs10808120	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1100046	0.82[ASN][1000 genomes]
rs11514917	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11768949	0.90[ASN][1000 genomes]
rs11972261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11978799	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs11981980	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs12537977	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap]
rs12666317	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs12668434	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs13221585	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13222980	0.90[ASN][1000 genomes]
rs13229214	0.84[ASN][1000 genomes]
rs13232194	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs13233521	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs13242493	0.93[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1541519	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs1608651	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17136090	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs1829957	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2222539	0.92[ASN][1000 genomes]
rs2228686	0.86[ASN][1000 genomes]
rs2298854	0.86[ASN][1000 genomes]
rs2411059	0.82[ASN][1000 genomes]
rs41501847	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4296965	0.82[ASN][1000 genomes]
rs4609128	0.95[ASN][1000 genomes]
rs4620204	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4729860	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729866	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729873	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6465876	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs6465878	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6945997	0.84[ASN][1000 genomes]
rs6946773	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs6947403	0.81[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6953980	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs6960428	0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6963104	0.89[ASW][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.86[AFR][1000 genomes]
rs6967790	0.81[LWK][hapmap]
rs6978630	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7458786	0.94[ASN][1000 genomes]
rs7779145	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs7780405	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7780981	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs7785272	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs7789252	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794668	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs7800548	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs7807055	0.95[ASN][1000 genomes]
rs847646	0.87[JPT][hapmap]
rs847647	0.81[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap]
rs847648	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs847649	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs847656	0.81[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap]
rs847658	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs869332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs952879	0.88[ASN][1000 genomes]
rs955992	0.94[ASN][1000 genomes]
rs9718453	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv5881	chr7:102610488-102655699	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3374257	chr7:102636550-102671589	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11976237	LRRC17	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102633400-102644600	Weak transcription	Aorta	Aorta
2	chr7:102633400-102650800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:102634200-102647800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:102640400-102666800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:102640600-102644400	Weak transcription	Gastric	stomach

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