Variant report

Variant	rs4728690
Chromosome Location	chr7:86854004-86854005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:86848280..86850705-chr7:86852526..86854510,2	MCF-7	breast:
2	chr7:86847064..86850471-chr7:86853838..86858493,7	MCF-7	breast:
3	chr7:86780836..86784567-chr7:86853269..86855303,3	K562	blood:

Variant related genes	Relation type
ENSG00000135164	Chromatin interaction
ENSG00000135185	Chromatin interaction
ENSG00000224046	Chromatin interaction
ENSG00000200397	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10085726	0.94[AMR][1000 genomes]
rs10228392	0.91[AMR][1000 genomes]
rs10245036	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10257953	0.91[AMR][1000 genomes]
rs10263920	0.95[JPT][hapmap]
rs10273826	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1058972	0.82[GIH][hapmap];0.95[JPT][hapmap]
rs1558050	0.95[JPT][hapmap];0.81[YRI][hapmap]
rs1574795	0.80[ASN][1000 genomes]
rs17698411	0.87[EUR][1000 genomes]
rs17766011	0.87[EUR][1000 genomes]
rs1859125	0.87[EUR][1000 genomes]
rs1859126	0.85[EUR][1000 genomes]
rs1859127	0.85[EUR][1000 genomes]
rs1859128	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1981536	0.87[EUR][1000 genomes]
rs2074757	0.88[GIH][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes]
rs2108271	0.91[AMR][1000 genomes]
rs2108272	0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[AMR][1000 genomes]
rs2190424	0.92[GIH][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes]
rs2286267	0.95[JPT][hapmap]
rs2286268	0.92[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs2373389	0.87[EUR][1000 genomes]
rs3747807	0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[AMR][1000 genomes]
rs3789251	0.88[GIH][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes]
rs3789252	0.88[AMR][1000 genomes]
rs3810883	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4140847	0.85[AMR][1000 genomes]
rs4236504	0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.82[YRI][hapmap]
rs4639442	0.86[AMR][1000 genomes]
rs4728686	0.88[GIH][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes]
rs4728688	0.80[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs4728689	0.94[AMR][1000 genomes]
rs56327053	0.87[EUR][1000 genomes]
rs6465092	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6465099	0.85[ASN][1000 genomes]
rs6942407	0.82[ASN][1000 genomes]
rs6957785	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs6958626	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6958797	0.87[EUR][1000 genomes]
rs6959152	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6964225	1.00[CEU][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs6966613	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6978590	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs739711	0.86[EUR][1000 genomes]
rs739712	0.86[EUR][1000 genomes]
rs744136	0.87[EUR][1000 genomes]
rs757159	0.84[JPT][hapmap]
rs757961	0.94[AMR][1000 genomes]
rs765968	0.88[AMR][1000 genomes]
rs7776634	0.95[JPT][hapmap]
rs7793356	0.95[JPT][hapmap];0.82[YRI][hapmap]
rs7800541	0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7810647	0.88[GIH][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes]
rs886318	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs886787	0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1016761	chr7:86758544-86914152	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv888676	chr7:86781423-86858824	Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv1026193	chr7:86790391-86856448	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv539003	chr7:86790391-86856448	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
10	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4728690	C7orf23	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86850600-86859600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:86850600-86860400	Weak transcription	Right Atrium	heart
3	chr7:86850800-86854800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:86853400-86854800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:86853400-86854800	Weak transcription	NHEK	skin
6	chr7:86853400-86855000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:86853600-86855000	Weak transcription	HMEC	breast
8	chr7:86853800-86855200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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