Variant report

Variant	rs2239469
Chromosome Location	chrX:153584885-153584886
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 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:153575523-153589154	A549	lung:	n/a	n/a
3	POLR2A	chrX:153584713-153584929	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chrX:153574999-153585143	GM12892	blood:	n/a	n/a
5	POLR2A	chrX:153575585-153584989	K562	blood:	n/a	n/a
6	POLR2A	chrX:153579800-153585641	GM12878	blood:	n/a	n/a
7	POLR2A	chrX:153584094-153585169	HepG2	liver:	n/a	n/a
8	POLR2A	chrX:153584739-153585231	HL-60	blood:	n/a	n/a
9	POLR2A	chrX:153584778-153587248	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chrX:153584568-153585157	K562	blood:	n/a	n/a
11	POLR2A	chrX:153574330-153589367	U87	brain:	n/a	n/a
12	POLR2A	chrX:153584308-153584973	HepG2	liver:	n/a	n/a
13	POLR2A	chrX:153575547-153585596	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chrX:153584744-153584989	A549	lung:	n/a	n/a
15	POLR2A	chrX:153584824-153591855	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chrX:153583046-153587390	ProgFib	skin:	n/a	n/a
17	POLR2A	chrX:153578998-153588066	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chrX:153574277-153591646	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chrX:153584616-153585161	GM12892	blood:	n/a	n/a
20	POLR2A	chrX:153584811-153584983	GM12891	blood:	n/a	n/a
21	POLR2A	chrX:153584585-153584922	K562	blood:	n/a	n/a
22	POLR2A	chrX:153584658-153585231	GM12892	blood:	n/a	n/a
23	POLR2A	chrX:153584735-153584934	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chrX:153575457-153589373	U87	brain:	n/a	n/a
25	POLR2A	chrX:153576474-153589174	K562	blood:	n/a	n/a
26	POLR2A	chrX:153584652-153585148	SK-N-MC	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153582292..153585319-chrX:153630744..153633913,3	K562	blood:
2	chrX:153582162..153585045-chrX:153627001..153630604,4	K562	blood:

No data

Variant related genes	Relation type
FLNA	TF binding region
ENSG00000207165	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000013563	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1130929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12007167	1.00[YRI][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[JPT][hapmap]
rs2070643	0.88[JPT][hapmap]
rs2070807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2283762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28602900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898494	1.00[CEU][hapmap];1.00[JPT][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[JPT][hapmap]
rs743549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[JPT][hapmap]
rs915942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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:153576600-153585400	Strong transcription	NH-A	brain
11	chrX:153576600-153587200	Strong transcription	Pancreas	Pancrea
12	chrX:153576600-153588600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chrX:153576600-153589800	Strong transcription	Fetal Thymus	thymus
14	chrX:153576600-153593400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chrX:153576600-153593600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chrX:153576600-153595200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chrX:153576600-153595200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chrX:153576600-153595400	Strong transcription	Osteobl	bone
19	chrX:153576600-153595800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chrX:153576600-153596400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chrX:153576600-153596400	Strong transcription	Thymus	Thymus
22	chrX:153576600-153596600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chrX:153576600-153596600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chrX:153576600-153596800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chrX:153576600-153598800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
26	chrX:153576600-153599800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chrX:153576800-153585400	Strong transcription	Lung	lung
28	chrX:153576800-153585800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chrX:153576800-153592600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chrX:153576800-153592600	Strong transcription	NHLF	lung
31	chrX:153576800-153594000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chrX:153576800-153594600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chrX:153576800-153596000	Strong transcription	Brain Germinal Matrix	brain
34	chrX:153576800-153596000	Strong transcription	Placenta Amnion	Placenta Amnion
35	chrX:153576800-153603600	ZNF genes & repeats	Fetal Brain Female	brain
36	chrX:153577000-153595200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chrX:153577000-153595600	Strong transcription	Aorta	Aorta
38	chrX:153577200-153586000	Strong transcription	Colon Smooth Muscle	Colon
39	chrX:153577200-153594400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chrX:153577200-153594400	Strong transcription	Dnd41	blood
41	chrX:153577200-153594600	Strong transcription	Adipose Nuclei	Adipose
42	chrX:153577200-153595600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chrX:153577400-153587000	Weak transcription	Fetal Kidney	kidney
44	chrX:153577400-153591400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
45	chrX:153577400-153595000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chrX:153577400-153596000	Strong transcription	Ovary	ovary
47	chrX:153577600-153590800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chrX:153577600-153594400	Strong transcription	Left Ventricle	heart
49	chrX:153577600-153595200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chrX:153577800-153593400	Strong transcription	Fetal Muscle Leg	muscle

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