Variant report

Variant	rs5942955
Chromosome Location	chrX:109763603-109763604
allele	C/G
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	POLR2A	chrX:109763199-109763714	H1-neurons	neurons:	n/a	n/a
2	REST	chrX:109762887-109763938	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chrX:109763515-109765026	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chrX:109763078-109763730	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chrX:109763602-109763782	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chrX:109763120-109763718	H1-neurons	neurons:	n/a	n/a
7	TAF1	chrX:109763575-109764317	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chrX:109763359-109764903	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGAG1-1	chrX:109763540-109766249	NR_002718

Variant related genes	Relation type
TDGF1P3	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10047014	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs10126502	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs12006849	1.00[CHB][hapmap]
rs12012172	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs12395955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12396834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12857107	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2016878	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2073785	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2073787	1.00[CHB][hapmap]
rs2206971	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2223782	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2404177	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5942660	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5942661	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5942674	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5942675	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5942676	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5942677	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5942678	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5942680	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5942681	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5942931	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5942953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs5943019	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5943044	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943045	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943046	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5943047	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943048	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5943050	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943051	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943052	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5943053	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs5943055	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943056	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5943057	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5985302	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5985519	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5985544	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs5985545	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs5985546	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7060124	0.85[CEU][hapmap];1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817233	chrX:109693720-110244649	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109762800-109763800	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chrX:109763000-109764000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chrX:109763000-109764200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chrX:109763200-109764800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chrX:109763400-109764200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chrX:109763400-109764200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chrX:109763400-109764400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chrX:109763600-109764200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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