Variant report

Variant	rs320999
Chromosome Location	chrX:77576690-77576691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10991	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs167674	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs2073176	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs2073178	0.86[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs2643581	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs320988	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs320990	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap]
rs320992	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs320995	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap]
rs320996	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs321005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs321028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs321029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs321073	0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs321074	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap]
rs321085	0.86[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs321086	0.86[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs321088	0.86[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs321090	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs321091	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs321094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs321095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs379704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs428207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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	nsv529299	chrX:77040316-77947157	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv532880	chrX:77085352-77769755	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv492122	chrX:77450503-77664330	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs320999	CYSLTR1	cis	lymphoblastoid	seeQTL
rs320999	GPR174	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:77572000-77576800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chrX:77572600-77578400	Weak transcription	Adipose Nuclei	Adipose
3	chrX:77576400-77576800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chrX:77576400-77576800	Enhancers	Dnd41	blood
5	chrX:77576400-77577000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chrX:77576400-77577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chrX:77576400-77577400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chrX:77576400-77577600	Enhancers	Primary T cells from cord blood	blood
9	chrX:77576400-77578000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chrX:77576400-77579400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chrX:77576400-77579400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chrX:77576400-77579600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chrX:77576400-77580200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chrX:77576400-77580600	Enhancers	Primary hematopoietic stem cells	blood
15	chrX:77576400-77580600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chrX:77576400-77581000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chrX:77576600-77576800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chrX:77576600-77577600	Enhancers	Primary B cells from cord blood	blood
19	chrX:77576600-77578400	Enhancers	Primary T cells fromperipheralblood	blood
20	chrX:77576600-77579000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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