Variant report

Variant	rs4870946
Chromosome Location	chr8:126603194-126603195
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:126601003..126603272-chr8:126603536..126606567,4	MCF-7	breast:
2	chr8:126593358..126595719-chr8:126599796..126603386,4	K562	blood:
3	chr8:126440732..126445779-chr8:126600349..126612045,20	MCF-7	breast:
4	chr8:126602958..126605776-chr8:126609153..126611231,2	MCF-7	breast:
5	chr8:126602321..126604094-chr8:126616027..126618273,2	MCF-7	breast:
6	chr8:126550463..126552355-chr8:126601119..126603239,2	MCF-7	breast:
7	chr8:126585008..126593535-chr8:126599853..126611131,18	MCF-7	breast:
8	chr8:126601013..126605207-chr8:126607092..126609721,3	MCF-7	breast:
9	chr8:126588355..126592631-chr8:126600736..126604091,3	MCF-7	breast:
10	chr8:126593642..126596532-chr8:126599701..126606279,16	MCF-7	breast:
11	chr8:126592991..126596537-chr8:126599819..126603670,10	MCF-7	breast:
12	chr8:126441094..126445421-chr8:126601055..126606149,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10086276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10086636	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10094725	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10111011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1031497	0.81[CEU][hapmap]
rs1031498	0.81[CEU][hapmap]
rs12334935	0.92[EUR][1000 genomes]
rs12386920	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12543922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546476	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12547829	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1454616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1454619	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs1454620	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1963945	0.81[CEU][hapmap]
rs28393360	0.90[EUR][1000 genomes]
rs28550378	0.96[EUR][1000 genomes]
rs4871618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871621	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6980895	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6981560	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6986030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6986139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6986305	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6996614	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6996809	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7001406	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7008590	1.00[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs7012744	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7012936	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729797	0.84[CEU][hapmap]
rs897158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs897161	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9297718	0.96[CEU][hapmap];0.94[EUR][1000 genomes]

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	nsv891437	chr8:126470817-126629328	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv6377	chr8:126579620-126639253	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv38	chr8:126593465-126639253	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1015513	chr8:126602536-126618074	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4870946	ZNF572	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126592600-126603800	Weak transcription	Pancreas	Pancrea
2	chr8:126600000-126604200	Weak transcription	Aorta	Aorta
3	chr8:126602200-126603400	Enhancers	GM12878-XiMat	blood
4	chr8:126602200-126603600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr8:126602200-126604400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:126602200-126606600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:126602200-126608600	Enhancers	Placenta	Placenta
8	chr8:126602400-126606800	Enhancers	NHEK	skin
9	chr8:126602400-126607400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr8:126602600-126605400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:126602600-126606800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:126602800-126603400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr8:126602800-126603800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr8:126602800-126607400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr8:126603000-126603400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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