Variant report

Variant	rs17282067
Chromosome Location	chrX:138973576-138973577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:138972047..138974366-chrX:139014308..139016435,2	MCF-7	breast:
2	chrX:138965466..138967928-chrX:138971445..138973731,2	MCF-7	breast:
3	chrX:138972307..138974912-chrX:138975339..138977928,3	K562	blood:
4	chrX:138964413..138967616-chrX:138972047..138974304,3	K562	blood:

Variant related genes	Relation type
ENSG00000221375	Chromatin interaction
ENSG00000101974	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12687833	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12688014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12688450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12688688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12688705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs12689199	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1361155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17281969	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17281990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17328640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17328647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17328703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17328709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2183251	1.00[CHB][hapmap]
rs2252290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2485722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs2485724	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs2485728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2485729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2491005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2491006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2491009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2497266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2497273	1.00[CHB][hapmap]
rs2497274	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2497277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2497281	1.00[CHB][hapmap]
rs2497282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2497284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2772194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2805901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4239992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs4363374	1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs4824924	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs5908669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5908746	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap]
rs5953621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5953643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap]
rs5953748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5953790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6528650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs6528651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs6654371	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs7061584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs7885696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17282067	ATP11C	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138941800-138988200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chrX:138949000-138978800	Weak transcription	Fetal Intestine Small	intestine
3	chrX:138955200-138973600	Weak transcription	Primary B cells from peripheral blood	blood
4	chrX:138956400-138975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chrX:138959800-138976400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chrX:138965600-138974800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chrX:138971400-138973800	Enhancers	NHDF-Ad	bronchial
8	chrX:138971400-138974200	Enhancers	Osteobl	bone
9	chrX:138971400-138974600	Enhancers	HUVEC	blood vessel
10	chrX:138971600-138974000	Enhancers	Muscle Satellite Cultured Cells	--
11	chrX:138971600-138974000	Enhancers	NH-A	brain
12	chrX:138971800-138973800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chrX:138971800-138974000	Enhancers	A549	lung
14	chrX:138971800-138975200	Enhancers	K562	blood
15	chrX:138972000-138973600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chrX:138972200-138973600	Weak transcription	GM12878-XiMat	blood
17	chrX:138972200-138974400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chrX:138972200-138974800	Enhancers	NHEK	skin
19	chrX:138972400-138973800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chrX:138972400-138974800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chrX:138972600-138973800	Weak transcription	HSMM	muscle
22	chrX:138972800-138974000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chrX:138972800-138974000	Enhancers	HMEC	breast
24	chrX:138973000-138973600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chrX:138973000-138973600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chrX:138973000-138973800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chrX:138973000-138973800	Enhancers	Colon Smooth Muscle	Colon
28	chrX:138973000-138984400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chrX:138973200-138974400	Weak transcription	NHLF	lung
30	chrX:138973400-138973800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chrX:138973400-138974000	Flanking Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links