Variant report

Variant	rs7675305
Chromosome Location	chr4:143519738-143519739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:143516751..143518964-chr4:143518967..143521709,2	MCF-7	breast:
2	chr4:143517546..143521080-chr4:143535706..143539870,4	MCF-7	breast:
3	chr4:143518531..143520300-chr4:143521688..143524164,2	MCF-7	breast:
4	chr4:143388165..143401257-chr4:143512284..143528837,40	MCF-7	breast:
5	chr4:143391752..143397700-chr4:143513549..143524281,24	MCF-7	breast:
6	chr4:143512089..143514343-chr4:143518901..143520578,2	MCF-7	breast:
7	chr4:143517914..143520098-chr4:143525876..143528126,2	MCF-7	breast:
8	chr4:143504828..143506931-chr4:143519506..143521581,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10020797	0.86[ASN][1000 genomes]
rs1017527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1019643	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]
rs1031104	0.94[CHD][hapmap]
rs10857396	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11100753	0.81[ASN][1000 genomes]
rs1116689	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937786	0.86[ASN][1000 genomes]
rs11942593	0.82[ASN][1000 genomes]
rs11943397	0.82[CHD][hapmap]
rs11944455	0.81[CHB][hapmap]
rs12163905	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12504610	0.86[ASN][1000 genomes]
rs12508480	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12509465	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12645567	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650777	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs13102826	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120964	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13129274	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13147451	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13150837	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1364925	0.83[CHD][hapmap]
rs1373035	0.82[ASN][1000 genomes]
rs1373038	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1373039	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1373040	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1425522	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]
rs1425523	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs1443184	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443189	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443190	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17016514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17016768	0.81[CHD][hapmap]
rs17729514	0.91[CEU][hapmap]
rs1814061	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1822363	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1838085	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1838087	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2008423	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2081474	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs2120159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2120160	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2197215	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331945	0.81[CHD][hapmap]
rs3967128	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4690722	0.87[ASN][1000 genomes]
rs6537122	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839894	0.89[CHB][hapmap]
rs6845652	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726477	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72728615	0.80[ASN][1000 genomes]
rs7376422	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7434560	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7437824	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs745719	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7666140	0.81[CHD][hapmap]
rs7670457	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7671783	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7682731	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685002	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7688435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894584	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs894585	0.95[ASN][1000 genomes]
rs962372	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs978361	0.94[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv830101	chr4:143518810-143684392	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7675305	C4orf49	cis	parietal	SCAN
rs7675305	POU4F2	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143507400-143520200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:143508200-143520000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr4:143511800-143521200	Weak transcription	Primary T cells from cord blood	blood
4	chr4:143514600-143519800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:143514800-143519800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:143516000-143523800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:143516400-143520400	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:143517000-143530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:143517400-143539400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:143518200-143520000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:143518400-143524200	Weak transcription	Aorta	Aorta
12	chr4:143518800-143520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:143519200-143519800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:143519200-143520000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:143519200-143520200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:143519200-143520200	Enhancers	Left Ventricle	heart
17	chr4:143519200-143520400	Enhancers	Pancreas	Pancrea
18	chr4:143519200-143520600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:143519400-143520600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:143519400-143520600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:143519400-143520800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
22	chr4:143519600-143521000	Weak transcription	Liver	Liver
23	chr4:143519600-143525000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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