Variant report

Variant	rs2070825
Chromosome Location	chrX:153581932-153581933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chrX:153576464-153589249	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chrX:153580861-153583634	K562	blood:	n/a	n/a
3	POLR2A	chrX:153575523-153589154	A549	lung:	n/a	n/a
4	POLR2A	chrX:153581774-153582056	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chrX:153579802-153583855	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chrX:153581330-153581959	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chrX:153581705-153582178	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chrX:153574999-153585143	GM12892	blood:	n/a	n/a
9	POLR2A	chrX:153575585-153584989	K562	blood:	n/a	n/a
10	POLR2A	chrX:153576484-153584591	HL-60	blood:	n/a	n/a
11	POLR2A	chrX:153580878-153582031	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chrX:153581003-153583806	MCF-7	breast:	n/a	n/a
13	POLR2A	chrX:153581320-153582666	HL-60	blood:	n/a	n/a
14	POLR2A	chrX:153581708-153582073	U87	brain:	n/a	n/a
15	POLR2A	chrX:153579800-153585641	GM12878	blood:	n/a	n/a
16	POLR2A	chrX:153581635-153581974	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chrX:153581805-153582073	U87	brain:	n/a	n/a
18	POLR2A	chrX:153581225-153584015	HepG2	liver:	n/a	n/a
19	POLR2A	chrX:153581221-153583048	GM12878	blood:	n/a	n/a
20	POLR2A	chrX:153574330-153589367	U87	brain:	n/a	n/a
21	POLR2A	chrX:153581680-153582040	A549	lung:	n/a	n/a
22	POLR2A	chrX:153580454-153582980	GM12892	blood:	n/a	n/a
23	MYC	chrX:153581829-153582001	MCF-7	breast:	n/a	n/a
24	POLR2A	chrX:153581105-153582974	HepG2	liver:	n/a	n/a
25	POLR2A	chrX:153575547-153585596	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chrX:153581772-153582134	GM12878	blood:	n/a	n/a
27	POLR2A	chrX:153581480-153582044	A549	lung:	n/a	n/a
28	POLR2A	chrX:153581846-153581943	GM12878	blood:	n/a	n/a
29	POLR2A	chrX:153578998-153588066	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chrX:153578818-153582979	ProgFib	skin:	n/a	n/a
31	POLR2A	chrX:153581456-153582102	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chrX:153574277-153591646	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chrX:153580261-153584530	GM12892	blood:	n/a	n/a
34	POLR2A	chrX:153581597-153581945	GM12878	blood:	n/a	n/a
35	POLR2A	chrX:153580934-153581992	A549	lung:	n/a	n/a
36	POLR2A	chrX:153581352-153582098	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chrX:153581621-153581964	K562	blood:	n/a	n/a
38	POLR2A	chrX:153581649-153582356	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chrX:153581717-153581951	MCF-7	breast:	n/a	n/a
40	POLR2A	chrX:153581408-153583050	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chrX:153581403-153582896	A549	lung:	n/a	n/a
42	POLR2A	chrX:153580878-153582077	GM12878	blood:	n/a	n/a
43	POLR2A	chrX:153581326-153582107	ECC-1	luminal epithelium:	n/a	n/a
44	PBX3	chrX:153581021-153582043	A549	lung:	n/a	chrX:153581590-153581599
45	POLR2A	chrX:153575457-153589373	U87	brain:	n/a	n/a
46	ZNF263	chrX:153581050-153581952	HEK293-T-REx	kidney:	n/a	n/a
47	POLR2A	chrX:153576474-153589174	K562	blood:	n/a	n/a
48	POLR2A	chrX:153569010-153584503	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153581360..153583456-chrX:153624842..153626588,3	K562	blood:
2	X:153574513-153584637..X:153719993-153730954	Hela-S3	cervix:
3	chrX:153580991..153583876-chrX:153626636..153628622,3	K562	blood:
4	chrX:153580371..153583201-chrX:153685549..153687642,2	MCF-7	breast:
5	X:153574513-153584637..X:153657611-153671976	H1-hESC	embryonic stem cell:	embryo
6	X:153574513-153584637..X:153614328-153625659	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
FLNA	TF binding region
ENSG00000130827	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000203879	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1130929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs12559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2051508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2070643	0.87[JPT][hapmap]
rs2070807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs2070819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2070821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs2070827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs2070829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2097214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2156911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2239469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs28602900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs4898484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6727	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs743547	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs743548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs743549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs762514	1.00[CEU][hapmap]
rs7886627	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs915941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs915942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531228	chrX:152864376-153609161	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv531227	chrX:152864376-153655730	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
3	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
4	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
5	nsv529439	chrX:153333946-153595528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv932632	chrX:153333946-153623000	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	nsv531232	chrX:153333946-153626120	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv531233	chrX:153333946-153626120	Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
9	nsv523072	chrX:153333946-153626738	Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
10	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
11	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
12	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
13	nsv9999	chrX:153567427-153621413	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
14	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153575600-153585000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chrX:153575800-153589000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chrX:153576000-153585800	Weak transcription	Small Intestine	intestine
4	chrX:153576000-153588200	Genic enhancers	A549	lung
5	chrX:153576000-153596000	Weak transcription	Primary hematopoietic stem cells	blood
6	chrX:153576200-153595800	Weak transcription	Right Atrium	heart
7	chrX:153576200-153596600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chrX:153576400-153587200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chrX:153576400-153599400	ZNF genes & repeats	Fetal Stomach	stomach
10	chrX:153576600-153582000	Genic enhancers	Primary B cells from peripheral blood	blood
11	chrX:153576600-153583800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chrX:153576600-153585400	Strong transcription	NH-A	brain
13	chrX:153576600-153587200	Strong transcription	Pancreas	Pancrea
14	chrX:153576600-153588600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chrX:153576600-153589800	Strong transcription	Fetal Thymus	thymus
16	chrX:153576600-153593400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chrX:153576600-153593600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chrX:153576600-153595200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chrX:153576600-153595200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chrX:153576600-153595400	Strong transcription	Osteobl	bone
21	chrX:153576600-153595800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chrX:153576600-153596400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chrX:153576600-153596400	Strong transcription	Thymus	Thymus
24	chrX:153576600-153596600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chrX:153576600-153596600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chrX:153576600-153596800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chrX:153576600-153598800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
28	chrX:153576600-153599800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chrX:153576800-153583800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chrX:153576800-153584000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chrX:153576800-153585400	Strong transcription	Lung	lung
32	chrX:153576800-153585800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chrX:153576800-153592600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chrX:153576800-153592600	Strong transcription	NHLF	lung
35	chrX:153576800-153594000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chrX:153576800-153594600	Strong transcription	Muscle Satellite Cultured Cells	--
37	chrX:153576800-153596000	Strong transcription	Brain Germinal Matrix	brain
38	chrX:153576800-153596000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chrX:153576800-153603600	ZNF genes & repeats	Fetal Brain Female	brain
40	chrX:153577000-153595200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chrX:153577000-153595600	Strong transcription	Aorta	Aorta
42	chrX:153577200-153582800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chrX:153577200-153583200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chrX:153577200-153586000	Strong transcription	Colon Smooth Muscle	Colon
45	chrX:153577200-153594400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chrX:153577200-153594400	Strong transcription	Dnd41	blood
47	chrX:153577200-153594600	Strong transcription	Adipose Nuclei	Adipose
48	chrX:153577200-153595600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chrX:153577400-153587000	Weak transcription	Fetal Kidney	kidney
50	chrX:153577400-153591400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood

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