Variant report

Variant	rs10248553
Chromosome Location	chr7:150317472-150317473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10216102	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10224387	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10232947	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10235151	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10239578	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10240209	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10253121	0.80[ASN][1000 genomes]
rs10255487	0.85[EUR][1000 genomes]
rs10270122	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10273606	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11763094	0.80[ASN][1000 genomes]
rs11971770	0.90[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs11975418	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11984138	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12671922	0.82[EUR][1000 genomes]
rs1317276	0.95[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1916027	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2140138	0.90[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2140139	0.80[EUR][1000 genomes]
rs2140145	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28537284	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28829297	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3088115	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3735085	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4143732	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56158089	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60628216	0.84[EUR][1000 genomes]
rs6464081	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs6959171	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6959264	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6961075	0.82[EUR][1000 genomes]
rs7357320	0.80[EUR][1000 genomes]
rs73727323	0.82[EUR][1000 genomes]
rs73727325	0.82[EUR][1000 genomes]
rs73727338	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7782221	0.80[EUR][1000 genomes]
rs7787987	0.80[EUR][1000 genomes]
rs7797456	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs7800143	0.82[EUR][1000 genomes]
rs7806724	0.95[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs952642	0.81[EUR][1000 genomes]
rs9640279	0.95[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10248553	GIMAP4	cis	parietal	SCAN
rs10248553	ATP6V0E2	cis	parietal	SCAN
rs10248553	TMEM176B	cis	cerebellum	SCAN
rs10248553	COL8A2	trans	parietal	SCAN
rs10248553	GIMAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150312400-150321800	Weak transcription	Dnd41	blood
2	chr7:150312600-150317600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:150312600-150317600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:150312800-150323000	Weak transcription	Fetal Thymus	thymus
5	chr7:150313400-150317600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:150315000-150322200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:150316800-150317600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr7:150316800-150317600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr7:150316800-150318000	Enhancers	HUVEC	blood vessel
10	chr7:150316800-150318800	Enhancers	Primary T cells from cord blood	blood
11	chr7:150316800-150318800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:150316800-150320400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:150316800-150320400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr7:150317000-150318000	Enhancers	GM12878-XiMat	blood
15	chr7:150317000-150319400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr7:150317000-150319800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:150317000-150321000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr7:150317200-150317600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:150317400-150317800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links