Variant report

Variant	rs2872817
Chromosome Location	chrX:153558418-153558419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:153553291..153556056-chrX:153556573..153558739,2	K562	blood:
2	chrX:153552129..153554532-chrX:153555776..153559558,3	MCF-7	breast:
3	chrX:153535574..153537491-chrX:153557115..153558763,2	K562	blood:
4	chrX:153556999..153558621-chrX:153598452..153600945,2	K562	blood:
5	chrX:153550078..153552907-chrX:153556234..153558933,2	K562	blood:

Variant related genes	Relation type
ENSG00000196924	Chromatin interaction
ENSG00000007350	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12007167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap]
rs17426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2070816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2070822	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs2239470	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs4446899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs4898478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4898479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs5945185	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs5945413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs5945423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs915943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv7161	chrX:153391266-153558551	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2872817	LAGE3	cis	lymphoblastoid	seeQTL
rs2872817	PLXNA3	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153554000-153559000	Enhancers	Fetal Muscle Leg	muscle
2	chrX:153555400-153558800	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chrX:153556000-153558600	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chrX:153556000-153558600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chrX:153556200-153561400	Weak transcription	Primary B cells from cord blood	blood
6	chrX:153556400-153559000	Enhancers	Primary T cells fromperipheralblood	blood
7	chrX:153556400-153561200	Weak transcription	Primary B cells from peripheral blood	blood
8	chrX:153556600-153562600	Weak transcription	Spleen	Spleen
9	chrX:153557400-153561600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chrX:153557600-153558600	Weak transcription	NHDF-Ad	bronchial
11	chrX:153557600-153558800	Bivalent Enhancer	Osteobl	bone
12	chrX:153557600-153561800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chrX:153557600-153562000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chrX:153557800-153559000	Enhancers	HSMMtube	muscle
15	chrX:153557800-153562200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chrX:153558000-153562000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chrX:153558200-153558600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chrX:153558200-153561800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chrX:153558200-153562000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chrX:153558400-153558600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chrX:153558400-153558600	Enhancers	Right Atrium	heart
22	chrX:153558400-153558800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chrX:153558400-153559000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
24	chrX:153558400-153559000	Enhancers	HSMM	muscle

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