Variant report

Variant	rs1019643
Chromosome Location	chr4:143503071-143503072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143500805..143505474-chr4:143506198..143510194,5	MCF-7	breast:
2	chr4:143395086..143396715-chr4:143501537..143504287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1017527	0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs10857396	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1116689	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12645567	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13120964	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13147451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13149611	0.90[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1373040	0.82[ASN][1000 genomes]
rs1425522	0.94[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];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1425523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1443190	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs17016514	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs17729514	0.91[CEU][hapmap]
rs2008423	0.82[ASN][1000 genomes]
rs2081474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2120159	0.90[CHB][hapmap]
rs2197215	0.82[ASN][1000 genomes]
rs6845652	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72726477	0.86[ASN][1000 genomes]
rs7376422	0.84[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7671783	0.89[CHB][hapmap]
rs7675305	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7682731	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7688435	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs894585	0.82[ASN][1000 genomes]
rs978361	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1019643	POU4F2	cis	cerebellum	SCAN
rs1019643	FAM73B	trans	cerebellum	SCAN
rs1019643	C4orf49	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143489600-143505600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr4:143489800-143519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143490600-143504600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:143490800-143519200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:143492400-143506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:143493600-143510800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:143496000-143503600	Weak transcription	Fetal Heart	heart
8	chr4:143496200-143505600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:143499200-143505400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:143500600-143503800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:143501400-143506200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:143501400-143506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:143501400-143511000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:143501600-143505600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:143502200-143505400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:143502800-143504200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:143502800-143504400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:143503000-143503800	Enhancers	Primary T helper cells fromperipheralblood	blood

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