Variant report

Variant	rs4824924
Chromosome Location	chrX:139019136-139019137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:139013572..139015266-chrX:139017160..139019267,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101974	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12688014	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs12688450	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs12688688	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs12688705	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs12689199	1.00[GIH][hapmap]
rs12689725	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs1338059	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs1361155	1.00[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs1415887	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs17281969	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17281990	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17282011	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs17282039	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs17282067	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs17282081	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs17328640	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17328647	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs17328703	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17328709	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2252290	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs2485721	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs2485722	1.00[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap]
rs2485728	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2485729	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs2485732	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2485733	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs2491005	0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs2491006	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2491009	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs2497266	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs2497274	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap]
rs2497277	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2497280	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs2497282	1.00[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs2497284	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs4239992	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs4363374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs5908669	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs5908746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.82[YRI][hapmap]
rs5953621	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs5953643	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs5953692	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5953748	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs5953790	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap]
rs5954529	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5954562	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs5954594	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs6528650	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap]
rs6528651	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs6654371	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs7061584	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs7885696	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[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	nsv532936	chrX:138687855-139384681	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv491760	chrX:138780768-139283477	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv917353	chrX:138912620-139283492	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4824924	STAT1	trans	brain	seeQTL
rs4824924	IFIT3	trans	brain	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:139017400-139019200	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chrX:139018400-139019400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chrX:139018400-139019600	Enhancers	H9 Cell Line	embryonic stem cell
4	chrX:139018600-139019200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chrX:139018600-139019400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chrX:139018600-139019400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chrX:139018600-139019600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chrX:139018800-139019200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chrX:139019000-139019800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chrX:139019000-139019800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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