Variant report

Variant	rs2485721
Chromosome Location	chrX:138963135-138963136
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	TCF12	chrX:138963006-138964334	SK-N-SH	brain:	n/a	n/a
2	EP300	chrX:138963033-138964277	SK-N-SH	brain:	n/a	chrX:138963240-138963254 chrX:138964071-138964085
3	CEBPB	chrX:138963082-138963441	Hela-S3	cervix:	n/a	chrX:138963239-138963252 chrX:138963239-138963250 chrX:138963241-138963252
4	MAX	chrX:138963121-138963710	SK-N-SH	brain:	n/a	chrX:138963145-138963154
5	FOSL2	chrX:138963094-138964299	SK-N-SH	brain:	n/a	chrX:138963224-138963235
6	CEBPB	chrX:138963052-138964215	IMR90	lung:	n/a	chrX:138963239-138963252 chrX:138963239-138963250 chrX:138963241-138963252
7	NFIC	chrX:138963135-138964326	SK-N-SH	brain:	n/a	n/a
8	GATA3	chrX:138962975-138964371	SK-N-SH	brain:	n/a	chrX:138963574-138963584
9	KAP1	chrX:138962822-138964059	U2OS	brain:	n/a	n/a
10	GATA2	chrX:138963037-138964391	HUVEC	blood vessel:	n/a	chrX:138963574-138963584
11	JUND	chrX:138963067-138963646	SK-N-SH	brain:	n/a	chrX:138963224-138963235
12	GATA3	chrX:138962965-138964436	SK-N-SH	brain:	n/a	chrX:138963574-138963584

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:138960226..138963595-chrX:138966113..138968474,3	K562	blood:
2	chrX:138961120..138966605-chrX:139013410..139016056,4	K562	blood:

Variant related genes	Relation type
RNU6ATAC23P	TF binding region
ENSG00000101974	Chromatin interaction
ENSG00000221375	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12687833	1.00[CHB][hapmap]
rs12688014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12688450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12688688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12688705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1361155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17281969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17281990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17282067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17328640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17328647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs17328703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17328709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2183251	1.00[CHB][hapmap]
rs2252290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs2485722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap]
rs2485724	1.00[CHB][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];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2491005	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2491006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2491009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2497266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2497273	1.00[CHB][hapmap]
rs2497274	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs2497277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2497281	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2497282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2497284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2772194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2805901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs4239992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4363374	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4824924	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs5908669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs5908746	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs5953621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs5953643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5953748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5953790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6528650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs6528651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs6635906	1.00[CHB][hapmap]
rs6654371	1.00[CEU][hapmap]
rs7061584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7885696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[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	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138934000-138964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chrX:138935600-138967600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chrX:138937000-138964200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chrX:138941600-138964200	Weak transcription	Primary T cells from cord blood	blood
5	chrX:138941800-138988200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chrX:138949000-138978800	Weak transcription	Fetal Intestine Small	intestine
7	chrX:138949600-138964600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chrX:138951400-138966600	Weak transcription	GM12878-XiMat	blood
9	chrX:138954400-138965600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chrX:138955200-138973600	Weak transcription	Primary B cells from peripheral blood	blood
11	chrX:138956400-138975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chrX:138956800-138964600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chrX:138957200-138963200	Enhancers	HUVEC	blood vessel
14	chrX:138958200-138963400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chrX:138959600-138964000	Weak transcription	Primary hematopoietic stem cells	blood
16	chrX:138959800-138976400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chrX:138960600-138964600	Weak transcription	Liver	Liver
18	chrX:138961200-138963200	Weak transcription	K562	blood
19	chrX:138961400-138963200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chrX:138962000-138964200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chrX:138962200-138963600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chrX:138962200-138964000	Enhancers	NHDF-Ad	bronchial
23	chrX:138962200-138965400	Enhancers	Hela-S3	cervix
24	chrX:138962200-138965400	Enhancers	Osteobl	bone
25	chrX:138962400-138963800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chrX:138962400-138964600	Enhancers	Fetal Heart	heart
27	chrX:138962400-138965000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chrX:138962400-138965400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chrX:138962400-138965600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chrX:138962600-138963800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chrX:138962800-138963400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chrX:138962800-138964000	Enhancers	NHLF	lung
33	chrX:138962800-138965000	Enhancers	Muscle Satellite Cultured Cells	--
34	chrX:138963000-138963400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chrX:138963000-138963800	Enhancers	NH-A	brain
36	chrX:138963000-138964400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chrX:138963000-138964800	Enhancers	NHEK	skin
38	chrX:138963000-138965000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chrX:138963000-138965000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chrX:138963000-138965000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chrX:138963000-138965200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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