Variant report

Variant	rs5912789
Chromosome Location	chrX:78423102-78423103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chrX:78423096-78423238	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF384	chrX:78422818-78423296	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
GPR174	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12845853	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3810711	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs3810712	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3827440	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs3827441	0.88[MEX][hapmap]
rs5912231	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5912736	0.94[JPT][hapmap]
rs5912790	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5912791	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs5912792	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5959237	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3394349	chrX:77977388-78779139	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932683	chrX:78373033-79166725	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869186	chrX:78392001-79166725	Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5912789	GPR23	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:78418000-78423200	Genic enhancers	Dnd41	blood
2	chrX:78418400-78426600	Weak transcription	Thymus	Thymus
3	chrX:78418400-78426800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chrX:78418600-78426800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chrX:78420200-78424000	Enhancers	Primary B cells from cord blood	blood
6	chrX:78420200-78424200	Enhancers	Primary B cells from peripheral blood	blood
7	chrX:78420800-78424600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chrX:78420800-78426600	Enhancers	Primary hematopoietic stem cells	blood
9	chrX:78421600-78423200	Enhancers	GM12878-XiMat	blood
10	chrX:78421800-78424000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chrX:78422200-78423200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chrX:78422200-78423200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chrX:78422200-78424000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chrX:78422400-78423400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chrX:78422400-78424000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chrX:78422600-78423200	Active TSS	Primary T cells fromperipheralblood	blood
17	chrX:78422600-78424000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chrX:78422600-78425800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chrX:78422800-78424000	Genic enhancers	Fetal Thymus	thymus
20	chrX:78422800-78427000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chrX:78423000-78423200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chrX:78423000-78423200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chrX:78423000-78423800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chrX:78423000-78433200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chrX:78423000-78439600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links