Variant report

Variant	rs12646630
Chromosome Location	chr4:21770028-21770029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:21769756..21770575-chr4:22358426..22359045,2	MCF-7	breast:
2	chr4:21765094..21766763-chr4:21768387..21770633,2	K562	blood:
3	chr4:21513660..21514733-chr4:21769803..21771071,4	MCF-7	breast:
4	chr4:21513547..21514492-chr4:21769669..21770605,6	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10002460	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10006785	0.98[ASN][1000 genomes]
rs10012055	0.80[GIH][hapmap]
rs10012747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs10016234	0.98[ASN][1000 genomes]
rs10028323	0.86[EUR][1000 genomes]
rs10031539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10034603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10938858	0.88[CHB][hapmap]
rs11734604	0.88[ASW][hapmap];0.81[LWK][hapmap]
rs12498561	0.88[CHB][hapmap]
rs12503736	0.88[CHB][hapmap]
rs12642578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1349384	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1380270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1459271	0.80[GIH][hapmap]
rs1459274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs1471221	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168625	0.88[CHB][hapmap]
rs17498679	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17498715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1809267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1827590	0.83[EUR][1000 genomes]
rs1827591	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap]
rs1841182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1841185	0.83[CHB][hapmap]
rs1841186	0.83[CHB][hapmap]
rs1968778	0.88[CHB][hapmap]
rs1985182	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1993037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007970	0.82[CHB][hapmap]
rs2007971	0.87[CHB][hapmap]
rs2018175	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]
rs2044809	0.82[ASW][hapmap]
rs28667579	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34833395	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs35609084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs6448070	0.83[EUR][1000 genomes]
rs6448072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6448073	0.84[EUR][1000 genomes]
rs6448075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs6840539	0.82[CHB][hapmap]
rs6856781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7375384	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs7378252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs7664617	0.83[CHB][hapmap]
rs896121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9291430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs966045	0.83[CHB][hapmap]
rs9884923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs9994945	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv4269	chr4:21761429-21806056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv980440	chr4:21765590-21771393	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12646630	ZCCHC4	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21766000-21771000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:21766600-21780200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:21769200-21770200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:21769400-21780400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:21770000-21770200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:21770000-21770200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr4:21770000-21770200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:21770000-21770200	Enhancers	Adipose Nuclei	Adipose
9	chr4:21770000-21770200	Enhancers	Liver	Liver
10	chr4:21770000-21770200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr4:21770000-21770200	Flanking Active TSS	HUVEC	blood vessel
12	chr4:21770000-21770400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:21770000-21771000	Enhancers	NH-A	brain
14	chr4:21770000-21771400	Enhancers	NHEK	skin
15	chr4:21770000-21771600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:21770000-21771600	Enhancers	HMEC	breast
17	chr4:21770000-21771600	Enhancers	Osteobl	bone

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