Variant report

Variant	rs499669
Chromosome Location	chrX:154442443-154442444
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:154441446..154445245-chrX:154462967..154466501,5	MCF-7	breast:
2	chrX:154441104..154443352-chrX:154443765..154447008,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155959	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11156600	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs11887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs12013168	0.89[CHB][hapmap]
rs1393999	0.91[CHB][hapmap]
rs3105275	0.91[CHB][hapmap];0.96[CHD][hapmap];0.94[MEX][hapmap]
rs3105276	0.91[CHB][hapmap]
rs35296872	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap]
rs480210	0.87[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap]
rs4893113	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs492622	0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs496740	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap]
rs499428	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs504984	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs507127	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs516396	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap]
rs519641	0.89[CHB][hapmap]
rs520145	0.91[CHB][hapmap]
rs523614	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs524609	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs525161	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs533001	0.91[CHB][hapmap]
rs542899	0.91[CHB][hapmap]
rs543054	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs544582	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs547724	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs559165	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs568396	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs573189	0.87[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[MEX][hapmap]
rs573572	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs5945282	0.87[ASW][hapmap]
rs5945296	0.87[ASW][hapmap]
rs5983697	1.00[CHB][hapmap]
rs5983764	0.91[CHB][hapmap]
rs5987090	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6567813	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs782769	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs965691	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916671	chrX:154418093-154560374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv532966	chrX:154418093-154721378	Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs499669	F8A1	cis	lymphoblastoid	seeQTL
rs499669	TMLHE	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154439600-154443600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chrX:154441400-154444000	Weak transcription	Thymus	Thymus
3	chrX:154441800-154443800	Weak transcription	GM12878-XiMat	blood
4	chrX:154441800-154443800	Weak transcription	HUVEC	blood vessel

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