Variant report

Variant	rs766420
Chromosome Location	chrX:153554404-153554405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chrX:153553818-153554508	MCF-7	breast:	n/a	n/a
2	KAP1	chrX:153552642-153554441	HEK293	kidney:	n/a	n/a
3	KAP1	chrX:153552684-153554964	U2OS	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chrX:153553264..153555915-chrX:153626596..153629140,2	MCF-7	breast:
2	chrX:153550633..153555849-chrX:153596435..153601807,5	K562	blood:
3	chrX:153552129..153554532-chrX:153555776..153559558,3	MCF-7	breast:
4	chrX:153551837..153554543-chrX:153597241..153599661,3	MCF-7	breast:

No data

Variant related genes	Relation type
TKTL1	TF binding region
ENSG00000147403	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000196924	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2239466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2239467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs2239468	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4898478	0.81[JPT][hapmap]
rs5987245	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs766419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[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

Variant related diseases (count:1)

Disease	PMID	Source
Bilirubin levels	19419973	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs766420	FAM3A	cis	multi-tissue	Pritchard
rs766420	PLXNA3	cis	multi-tissue	Pritchard
rs766420	LAGE3	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153546200-153555600	Weak transcription	Spleen	Spleen
2	chrX:153550400-153554800	Weak transcription	Primary B cells from cord blood	blood
3	chrX:153550600-153556400	Weak transcription	Right Ventricle	heart
4	chrX:153551600-153555600	Weak transcription	GM12878-XiMat	blood
5	chrX:153552200-153554600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chrX:153553400-153554600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chrX:153553400-153554800	Enhancers	Colon Smooth Muscle	Colon
8	chrX:153553400-153555200	Enhancers	Primary T cells fromperipheralblood	blood
9	chrX:153553400-153555200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chrX:153553400-153557600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chrX:153553600-153554600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chrX:153553600-153555000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chrX:153553600-153555000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chrX:153553600-153555800	Enhancers	HUVEC	blood vessel
15	chrX:153553600-153558000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chrX:153553800-153554600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chrX:153553800-153554600	Weak transcription	Fetal Kidney	kidney
18	chrX:153553800-153554800	Enhancers	Primary T cells from cord blood	blood
19	chrX:153553800-153554800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chrX:153553800-153554800	Weak transcription	Left Ventricle	heart
21	chrX:153553800-153555400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chrX:153553800-153555600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chrX:153553800-153555800	Weak transcription	Right Atrium	heart
24	chrX:153554000-153554600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chrX:153554000-153556800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chrX:153554000-153559000	Enhancers	Fetal Muscle Leg	muscle
27	chrX:153554200-153558000	Enhancers	Fetal Thymus	thymus
28	chrX:153554400-153555000	Weak transcription	Fetal Stomach	stomach
29	chrX:153554400-153556400	Enhancers	Primary B cells from peripheral blood	blood

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