Variant report

Variant	rs2497284
Chromosome Location	chrX:138964271-138964272
allele	C/T
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	STAT3	chrX:138963738-138964465	MCF10A-Er-Src	breast:	n/a	chrX:138964040-138964051 chrX:138964026-138964035
4	FOS	chrX:138963816-138964425	HUVEC	blood vessel:	n/a	n/a
5	FOSL2	chrX:138963094-138964299	SK-N-SH	brain:	n/a	chrX:138963224-138963235
6	NFIC	chrX:138963135-138964326	SK-N-SH	brain:	n/a	n/a
7	PBX3	chrX:138963147-138964336	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chrX:138963746-138964456	MCF10A-Er-Src	breast:	n/a	n/a
9	EP300	chrX:138963604-138964336	SK-N-SH	brain:	n/a	chrX:138964071-138964085
10	GATA3	chrX:138962975-138964371	SK-N-SH	brain:	n/a	chrX:138963574-138963584
11	GATA2	chrX:138963037-138964391	HUVEC	blood vessel:	n/a	chrX:138963574-138963584
12	JUND	chrX:138963639-138964306	SK-N-SH	brain:	n/a	n/a
13	JUND	chrX:138963674-138964405	SK-N-SH	brain:	n/a	n/a
14	STAT3	chrX:138963281-138964463	MCF10A-Er-Src	breast:	n/a	chrX:138964040-138964051 chrX:138964026-138964035
15	STAT3	chrX:138963405-138964505	MCF10A-Er-Src	breast:	n/a	chrX:138964040-138964051 chrX:138964026-138964035 chrX:138964480-138964488
16	TCF12	chrX:138963203-138964370	SK-N-SH	brain:	n/a	n/a
17	GATA3	chrX:138962965-138964436	SK-N-SH	brain:	n/a	chrX:138963574-138963584
18	PBX3	chrX:138963173-138964338	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chrX:138961120..138966605-chrX:139013410..139016056,4	K562	blood:
2	chrX:138958237..138961195-chrX:138963345..138965697,2	K562	blood:
3	chrX:138963579..138966404-chrX:138996859..138999104,2	K562	blood:
4	chrX:138963632..138966605-chrX:139014337..139016021,2	K562	blood:
5	chrX:138963273..138965824-chrX:139016270..139017818,2	K562	blood:

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

Extended variants
information (count: 65 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12687833	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12688014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12688450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12688688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12688705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12689199	1.00[GIH][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1361155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17281969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17281990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17282067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328647	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap]
rs17328703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17328709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2183251	1.00[CHB][hapmap]
rs2252290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2485721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2485722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap]
rs2485724	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs2485728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485729	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][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];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap]
rs2491009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs2497266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs2497273	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2497274	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap]
rs2497277	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2497281	1.00[CHB][hapmap]
rs2497282	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2772194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs2805901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4239992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4363374	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs4824924	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]
rs5908669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs5908746	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs5953621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs5953643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs5953748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5953790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6528650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs6528651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs6635906	1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap]
rs6654371	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap]
rs7061584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs7885696	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][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:47 , 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:138941800-138988200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chrX:138949000-138978800	Weak transcription	Fetal Intestine Small	intestine
5	chrX:138949600-138964600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chrX:138951400-138966600	Weak transcription	GM12878-XiMat	blood
7	chrX:138954400-138965600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chrX:138955200-138973600	Weak transcription	Primary B cells from peripheral blood	blood
9	chrX:138956400-138975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chrX:138956800-138964600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chrX:138959800-138976400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chrX:138960600-138964600	Weak transcription	Liver	Liver
13	chrX:138962200-138965400	Enhancers	Hela-S3	cervix
14	chrX:138962200-138965400	Enhancers	Osteobl	bone
15	chrX:138962400-138964600	Enhancers	Fetal Heart	heart
16	chrX:138962400-138965000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chrX:138962400-138965400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chrX:138962400-138965600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chrX:138962800-138965000	Enhancers	Muscle Satellite Cultured Cells	--
20	chrX:138963000-138964400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chrX:138963000-138964800	Enhancers	NHEK	skin
22	chrX:138963000-138965000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chrX:138963000-138965000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chrX:138963000-138965000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chrX:138963000-138965200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chrX:138963200-138964400	Enhancers	K562	blood
27	chrX:138963200-138964600	Flanking Active TSS	HUVEC	blood vessel
28	chrX:138963200-138965000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chrX:138963400-138964600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chrX:138963400-138964800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chrX:138963400-138964800	Enhancers	Adipose Nuclei	Adipose
32	chrX:138963400-138965000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chrX:138963600-138964400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chrX:138963600-138964600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chrX:138963600-138964800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chrX:138963800-138964400	Flanking Active TSS	NH-A	brain
37	chrX:138964000-138964400	Flanking Active TSS	NHDF-Ad	bronchial
38	chrX:138964000-138964400	Weak transcription	NHLF	lung
39	chrX:138964000-138965200	Enhancers	Primary hematopoietic stem cells	blood
40	chrX:138964200-138964400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chrX:138964200-138964400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chrX:138964200-138964400	Enhancers	Primary T cells from cord blood	blood
43	chrX:138964200-138964600	Enhancers	Colon Smooth Muscle	Colon
44	chrX:138964200-138965000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chrX:138964200-138965200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chrX:138964200-138965200	Enhancers	Ovary	ovary
47	chrX:138964200-138965400	Enhancers	HUES64 Cell Line	embryonic stem cell

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