Variant report

Variant	rs2018175
Chromosome Location	chr4:21754408-21754409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10002460	0.87[EUR][1000 genomes]
rs10012055	0.80[GIH][hapmap]
rs10012747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028323	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031539	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10034603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938858	0.88[CHB][hapmap]
rs12498561	0.88[CHB][hapmap]
rs12503736	0.88[CHB][hapmap]
rs12642578	0.86[EUR][1000 genomes]
rs12646630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1349384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs1380270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459271	0.80[GIH][hapmap]
rs1459274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471221	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1562815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs168625	0.88[CHB][hapmap]
rs17498679	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs17498715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs1809267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs1827590	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827591	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1841181	0.84[YRI][hapmap]
rs1841182	0.86[EUR][1000 genomes]
rs1841185	0.83[CHB][hapmap]
rs1841186	0.83[CHB][hapmap]
rs1968778	0.88[CHB][hapmap]
rs1985182	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1993037	0.86[EUR][1000 genomes]
rs2007970	0.82[CHB][hapmap]
rs2007971	0.87[CHB][hapmap]
rs2017960	0.83[YRI][hapmap]
rs28667579	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34833395	0.83[CHB][hapmap]
rs35609084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4101631	0.99[ASN][1000 genomes]
rs4282162	0.88[CHB][hapmap]
rs4377576	0.88[CHB][hapmap]
rs4563486	0.88[CHB][hapmap]
rs6448069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448070	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448073	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838654	0.84[YRI][hapmap]
rs6838747	0.84[YRI][hapmap]
rs6840539	0.82[CHB][hapmap]
rs6856781	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs7375384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7378252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664617	0.83[CHB][hapmap]
rs896121	0.86[EUR][1000 genomes]
rs9291430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966045	0.83[CHB][hapmap]
rs9884923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs9994945	0.87[CHB][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	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv878751	chr4:21712050-21793807	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2018175	ZCCHC4	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21751600-21755200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:21752200-21754600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:21752200-21764600	Weak transcription	HMEC	breast
4	chr4:21752400-21755000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:21753200-21754800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:21753200-21755200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:21753600-21755200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:21754000-21754800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:21754000-21755000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr4:21754000-21755400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:21754000-21755600	Enhancers	Fetal Heart	heart
12	chr4:21754200-21755000	Weak transcription	Ovary	ovary
13	chr4:21754200-21755800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:21754400-21755000	Enhancers	Fetal Lung	lung
15	chr4:21754400-21755400	Enhancers	Colon Smooth Muscle	Colon

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