Variant report

Variant	rs1263240
Chromosome Location	chrX:73564051-73564052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:269)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:269 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chrX:73563940-73564090	AG09319	gingival:	n/a	n/a
2	CTCF	chrX:73563980-73564130	AoAF	blood vessel:	n/a	n/a
3	CTCF	chrX:73563829-73564227	IMR90	lung:	n/a	n/a
4	CTCF	chrX:73563812-73564199	A549	lung:	n/a	n/a
5	CTCF	chrX:73564020-73564170	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chrX:73563960-73564110	GM12875	blood:	n/a	n/a
7	CTCF	chrX:73563936-73564152	GM13977	blood:	n/a	n/a
8	CTCF	chrX:73564000-73564150	AG09309	skin:	n/a	n/a
9	RAD21	chrX:73563890-73564192	GM12878	blood:	n/a	n/a
10	CTCF	chrX:73563902-73564163	MCF-7	breast:	n/a	n/a
11	EP300	chrX:73563653-73564185	A549	lung:	n/a	n/a
12	TAF7	chrX:73563834-73564116	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chrX:73563838-73564274	A549	lung:	n/a	n/a
14	CTCF	chrX:73564000-73564150	GM12864	blood:	n/a	n/a
15	STAT3	chrX:73563943-73564198	GM12878	blood:	n/a	n/a
16	STAT3	chrX:73563709-73564111	MCF10A-Er-Src	breast:	n/a	n/a
17	SPI1	chrX:73563705-73564178	GM12878	blood:	n/a	n/a
18	CTCF	chrX:73564040-73564190	HAc	cerebellar:	n/a	n/a
19	SPI1	chrX:73563764-73564130	GM12891	blood:	n/a	n/a
20	CTCF	chrX:73563940-73564090	K562	blood:	n/a	n/a
21	CTCF	chrX:73563861-73564277	A549	lung:	n/a	n/a
22	RAD21	chrX:73563802-73564299	HCT-116	colon:	n/a	n/a
23	TCF7L2	chrX:73563824-73564105	PANC-1	pancreas:	n/a	n/a
24	EBF1	chrX:73563706-73564076	GM12878	blood:	n/a	chrX:73563893-73563904
25	CUX1	chrX:73563967-73564172	GM12878	blood:	n/a	chrX:73564099-73564115
26	TBP	chrX:73563757-73564169	Hela-S3	cervix:	n/a	n/a
27	RAD21	chrX:73563833-73564228	GM12878	blood:	n/a	n/a
28	CTCF	chrX:73563912-73564197	Pancreas_OC	pancreas:	n/a	n/a
29	CTCF	chrX:73563960-73564110	GM12872	blood:	n/a	n/a
30	RAD21	chrX:73563740-73564249	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chrX:73563784-73564282	HCT-116	colon:	n/a	n/a
32	HDAC2	chrX:73563769-73564110	MCF-7	breast:	n/a	n/a
33	CTCF	chrX:73563940-73564090	Hela-S3	cervix:	n/a	n/a
34	RAD21	chrX:73563860-73564166	GM12878	blood:	n/a	n/a
35	CTCF	chrX:73563940-73564090	HRE	kidney:	n/a	n/a
36	CTCF	chrX:73563917-73564134	NHEK	skin:	n/a	n/a
37	GATA3	chrX:73563562-73564316	A549	lung:	n/a	n/a
38	CEBPB	chrX:73563699-73564161	A549	lung:	n/a	n/a
39	RAD21	chrX:73563809-73564255	ECC-1	luminal epithelium:	n/a	n/a
40	EBF1	chrX:73563757-73564117	GM12878	blood:	n/a	chrX:73563893-73563904
41	SMC3	chrX:73563627-73564590	SK-N-SH	brain:	n/a	n/a
42	ZNF384	chrX:73563866-73564208	K562	blood:	n/a	n/a
43	CTCF	chrX:73563960-73564110	BE2_C	brain:	n/a	n/a
44	CTCF	chrX:73563914-73564165	K562	blood:	n/a	n/a
45	CTCF	chrX:73563980-73564130	RPTEC	kidney:	n/a	n/a
46	CTCF	chrX:73563960-73564110	HMEC	breast:	n/a	n/a
47	ZNF143	chrX:73563846-73564184	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chrX:73563923-73564152	HepG2	liver:	n/a	n/a
49	SPI1	chrX:73563814-73564072	GM12891	blood:	n/a	n/a
50	CTCF	chrX:73563920-73564070	WI-38	lung:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:73075052..73075793-chrX:73563582..73564389,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226515	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10855819	0.94[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs1151599	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1151602	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1263243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1263244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1263259	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12835261	1.00[JPT][hapmap]
rs1341326	1.00[JPT][hapmap]
rs174164	1.00[JPT][hapmap]
rs2066449	1.00[JPT][hapmap]
rs34974916	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs473645	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs486337	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs486485	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs499282	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs527480	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs557647	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs575348	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs5937811	0.85[ASW][hapmap];0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs5981268	1.00[JPT][hapmap]
rs5981594	1.00[JPT][hapmap]
rs5981595	1.00[JPT][hapmap]
rs5981614	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3364045	chrX:72896383-73699363	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	301 gene(s)	inside rSNPs	diseases
2	nsv916758	chrX:73546406-74420929	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv520605	chrX:73549327-73569476	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2830082	chrX:73564051-73635867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:73562600-73564200	Enhancers	Stomach Mucosa	stomach
2	chrX:73562600-73564600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chrX:73562800-73564600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chrX:73562800-73564600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chrX:73562800-73564600	Enhancers	Hela-S3	cervix
6	chrX:73563200-73564400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chrX:73563200-73564600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chrX:73563200-73564600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chrX:73563200-73564600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chrX:73563400-73564200	Enhancers	Adipose Nuclei	Adipose
11	chrX:73563400-73564200	Enhancers	Osteobl	bone
12	chrX:73563600-73564200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chrX:73563600-73564600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chrX:73563600-73568800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chrX:73563800-73564400	Enhancers	Primary B cells from peripheral blood	blood
16	chrX:73563800-73564400	Enhancers	A549	lung
17	chrX:73564000-73564400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chrX:73564000-73565400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chrX:73564000-73565600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links