Variant report

Variant	rs10224387
Chromosome Location	chr7:150313416-150313417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10216102	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10232947	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10235151	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10239578	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10240209	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10248553	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10255487	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10270122	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10273606	0.86[CEU][hapmap]
rs11763094	0.81[AFR][1000 genomes]
rs11971770	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs11975418	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11984138	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317276	0.86[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs1916027	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2140138	0.81[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs2140145	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28537284	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28829297	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3088115	0.88[ASW][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap]
rs3735085	0.82[ASW][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap]
rs4143732	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56158089	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57269277	0.81[AFR][1000 genomes]
rs60628216	0.80[EUR][1000 genomes]
rs6464081	0.81[CEU][hapmap]
rs6959171	0.86[CEU][hapmap]
rs6959264	0.86[CEU][hapmap]
rs73727338	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7797456	0.80[CEU][hapmap]
rs7800143	0.82[AMR][1000 genomes]
rs7806724	0.85[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs9640279	0.86[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3388935	chr7:150301204-150374532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10224387	GIMAP4	cis	parietal	SCAN
rs10224387	TMEM176B	cis	cerebellum	SCAN
rs10224387	ATP6V0E2	cis	parietal	SCAN
rs10224387	LR8	cis	multi-tissue	Pritchard
rs10224387	HCA112	cis	multi-tissue	Pritchard
rs10224387	COL8A2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150300600-150316800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:150312000-150314800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr7:150312200-150317000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr7:150312400-150317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:150312400-150321800	Weak transcription	Dnd41	blood
6	chr7:150312600-150317600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:150312600-150317600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:150312800-150314400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:150312800-150317200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr7:150312800-150323000	Weak transcription	Fetal Thymus	thymus
11	chr7:150313200-150316800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:150313400-150313600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:150313400-150317600	Weak transcription	Primary T cells fromperipheralblood	blood

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