Variant report

Variant	rs5987245
Chromosome Location	chrX:153551383-153551384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chrX:153551320-153551470	Hela-S3	cervix:	n/a	n/a
2	CTCF	chrX:153551380-153551530	MCF-7	breast:	n/a	n/a
3	CTCF	chrX:153551240-153551390	Hela-S3	cervix:	n/a	n/a
4	CTCF	chrX:153551340-153551490	K562	blood:	n/a	n/a
5	CTCF	chrX:153551340-153551490	MCF-7	breast:	n/a	n/a
6	CTCF	chrX:153551340-153551490	GM12872	blood:	n/a	n/a
7	CTCF	chrX:153551380-153551530	GM12873	blood:	n/a	n/a
8	RAD21	chrX:153551313-153551485	K562	blood:	n/a	n/a
9	CTCF	chrX:153551362-153551451	GM12891	blood:	n/a	n/a
10	CTCF	chrX:153551360-153551510	GM12873	blood:	n/a	n/a
11	CTCF	chrX:153551340-153551490	GM12873	blood:	n/a	n/a
12	CTCF	chrX:153551300-153551450	WERI-Rb-1	eye:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	X:153537523-153552005..X:153719993-153730954	K562	blood:
2	chrX:153538397..153540810-chrX:153549954..153551675,2	K562	blood:
3	chrX:153550078..153552907-chrX:153556234..153558933,2	K562	blood:
4	X:153537523-153552005..X:153614328-153625659	GM12878	blood:
5	chrX:153550633..153555849-chrX:153596435..153601807,5	K562	blood:

No data

Variant related genes	Relation type
TKTL1	TF binding region
ENSG00000196924	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000264631	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2239466	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2239467	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs2239468	1.00[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs6655282	1.00[JPT][hapmap]
rs766419	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs766420	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][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
rs5987245	FAM3A	cis	multi-tissue	Pritchard
rs5987245	PLXNA3	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153546000-153553800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chrX:153546200-153553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chrX:153546200-153553400	Weak transcription	Hela-S3	cervix
4	chrX:153546200-153555600	Weak transcription	Spleen	Spleen
5	chrX:153548200-153551600	Enhancers	GM12878-XiMat	blood
6	chrX:153548400-153551600	Enhancers	Primary B cells from peripheral blood	blood
7	chrX:153549800-153553800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chrX:153549800-153554000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chrX:153550400-153553400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chrX:153550400-153553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chrX:153550400-153553600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chrX:153550400-153553600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chrX:153550400-153553600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chrX:153550400-153553800	Weak transcription	Primary T cells from cord blood	blood
15	chrX:153550400-153553800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chrX:153550400-153553800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chrX:153550400-153554200	Weak transcription	Fetal Thymus	thymus
18	chrX:153550400-153554800	Weak transcription	Primary B cells from cord blood	blood
19	chrX:153550600-153553400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chrX:153550600-153556400	Weak transcription	Right Ventricle	heart

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