Variant report

Variant	rs12392447
Chromosome Location	chrX:153724351-153724352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:38)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	X:153649561-153657611..X:153719993-153730954	Hela-S3	cervix:
2	X:153681712-153701576..X:153719993-153730954	Hela-S3	cervix:
3	X:153719993-153730954..X:153994716-154000894	K562	blood:
4	chrX:153722923..153725739-chrX:153743923..153746815,2	MCF-7	breast:
5	X:153719993-153730954..X:154002691-154005706	K562	blood:
6	X:153574513-153584637..X:153719993-153730954	Hela-S3	cervix:
7	chrX:153625784..153628444-chrX:153721433..153724368,3	K562	blood:
8	X:153537523-153552005..X:153719993-153730954	K562	blood:
9	X:153648319-153649200..X:153719993-153730954	K562	blood:
10	X:153676883-153681712..X:153719993-153730954	Hela-S3	cervix:
11	X:153719993-153730954..X:154298909-154305587	K562	blood:
12	chrX:153721900..153725529-chrX:153738653..153743777,6	K562	blood:
13	X:153198557-153214268..X:153719993-153730954	H1-hESC	embryonic stem cell:	embryo
14	X:153719993-153730954..X:153989469-153994716	K562	blood:
15	X:153240638-153254508..X:153719993-153730954	Hela-S3	cervix:
16	X:153284529-153289470..X:153719993-153730954	K562	blood:
17	X:153719993-153730954..X:153755323-153771683	K562	blood:
18	chrX:153713080..153721291-chrX:153722442..153727868,15	K562	blood:
19	X:153719993-153730954..X:154015910-154019964	K562	blood:
20	chrX:153722760..153725293-chrX:153735134..153737436,2	MCF-7	breast:
21	X:153625659-153635385..X:153719993-153730954	GM12878	blood:
22	X:153190397-153198557..X:153719993-153730954	K562	blood:
23	X:153719993-153730954..X:154013320-154015910	K562	blood:
24	chrX:153711607..153725784-chrX:153738770..153748754,27	K562	blood:
25	X:153214268-153230257..X:153719993-153730954	K562	blood:
26	chrX:153721124..153725874-chrX:153733125..153737567,6	K562	blood:
27	X:153126719-153139428..X:153719993-153730954	K562	blood:
28	X:153272101-153284529..X:153719993-153730954	K562	blood:
29	X:153635385-153648319..X:153719993-153730954	K562	blood:
30	X:153586280-153597086..X:153719993-153730954	Hela-S3	cervix:
31	X:153532787-153537523..X:153719993-153730954	K562	blood:
32	X:153719993-153730954..X:154000894-154002691	H1-hESC	embryonic stem cell:	embryo
33	X:153360692-153365301..X:153719993-153730954	K562	blood:
34	X:153307734-153315090..X:153719993-153730954	K562	blood:
35	chrX:153626882..153628444-chrX:153722553..153724368,2	K562	blood:
36	X:153187063-153190397..X:153719993-153730954	Hela-S3	cervix:
37	X:153719993-153730954..X:154027387-154034565	K562	blood:
38	X:153182878-153187063..X:153719993-153730954	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC10A3-2	chrX:153724167-153724463	NONHSAT139193

No data

Variant related genes	Relation type
ENSG00000261773	Chromatin interaction
ENSG00000197180	Chromatin interaction
ENSG00000211524	Chromatin interaction
ENSG00000102032	Chromatin interaction
ENSG00000130827	Chromatin interaction
ENSG00000185515	Chromatin interaction
ENSG00000130830	Chromatin interaction
ENSG00000169057	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000206693	Chromatin interaction
ENSG00000102030	Chromatin interaction
ENSG00000102125	Chromatin interaction
ENSG00000182712	Chromatin interaction
ENSG00000071859	Chromatin interaction
ENSG00000177854	Chromatin interaction
ENSG00000126903	Chromatin interaction
ENSG00000007350	Chromatin interaction
ENSG00000184216	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000172534	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000130826	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000265176	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000206948	Chromatin interaction
ENSG00000214827	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000089820	Chromatin interaction
ENSG00000198910	Chromatin interaction
ENSG00000073009	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1050047	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap]
rs17052003	0.81[CEU][hapmap]
rs2071429	0.91[CEU][hapmap]
rs2315325	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap]
rs2472393	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[TSI][hapmap]
rs2472394	0.81[CEU][hapmap]
rs4542114	0.86[CHB][hapmap];1.00[GIH][hapmap]
rs4898389	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs5945100	0.90[CEU][hapmap]
rs5945195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs5945218	0.81[CEU][hapmap]
rs5945429	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs5945431	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap]
rs5945433	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs5945434	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs5986979	1.00[CHB][hapmap]
rs5986981	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs5987266	0.91[CEU][hapmap]
rs5987267	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs7051615	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap]
rs7057286	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap]
rs7879049	0.81[CEU][hapmap]
rs7886727	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
8	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153720000-153725200	Weak transcription	Primary B cells from peripheral blood	blood
2	chrX:153720000-153733400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chrX:153720000-153733600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chrX:153720200-153725000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chrX:153722000-153734000	Weak transcription	Pancreas	Pancrea
6	chrX:153723000-153724600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chrX:153723200-153724600	Flanking Active TSS	K562	blood
8	chrX:153724000-153727000	Enhancers	GM12878-XiMat	blood
9	chrX:153724200-153733400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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