Variant report

Variant	rs2239466
Chromosome Location	chrX:153554883-153554884
allele	A/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:153554829-153555052	HUVEC	blood vessel:	n/a	n/a
2	KAP1	chrX:153552684-153554964	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153553264..153555915-chrX:153626596..153629140,2	MCF-7	breast:
2	chrX:153550633..153555849-chrX:153596435..153601807,5	K562	blood:

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: 2 )

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

rs_ID	r²[population]
rs2239467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs2239468	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4898478	0.81[JPT][hapmap]
rs5987245	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs766419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs766420	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]

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
rs2239466	PLXNA3	cis	multi-tissue	Pritchard
rs2239466	FAM3A	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153546200-153555600	Weak transcription	Spleen	Spleen
2	chrX:153550600-153556400	Weak transcription	Right Ventricle	heart
3	chrX:153551600-153555600	Weak transcription	GM12878-XiMat	blood
4	chrX:153553400-153555200	Enhancers	Primary T cells fromperipheralblood	blood
5	chrX:153553400-153555200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chrX:153553400-153557600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chrX:153553600-153555000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chrX:153553600-153555000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chrX:153553600-153555800	Enhancers	HUVEC	blood vessel
10	chrX:153553600-153558000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chrX:153553800-153555400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chrX:153553800-153555600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chrX:153553800-153555800	Weak transcription	Right Atrium	heart
14	chrX:153554000-153556800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chrX:153554000-153559000	Enhancers	Fetal Muscle Leg	muscle
16	chrX:153554200-153558000	Enhancers	Fetal Thymus	thymus
17	chrX:153554400-153555000	Weak transcription	Fetal Stomach	stomach
18	chrX:153554400-153556400	Enhancers	Primary B cells from peripheral blood	blood
19	chrX:153554600-153555400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chrX:153554600-153555400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chrX:153554600-153555600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chrX:153554600-153555600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chrX:153554600-153555800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chrX:153554600-153556000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chrX:153554600-153556000	Enhancers	Fetal Kidney	kidney
26	chrX:153554600-153556600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chrX:153554800-153555200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chrX:153554800-153555400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chrX:153554800-153555800	Enhancers	Thymus	Thymus
30	chrX:153554800-153556000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chrX:153554800-153556200	Enhancers	Primary B cells from cord blood	blood
32	chrX:153554800-153556400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chrX:153554800-153557600	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links