Variant report

Variant	rs10956253
Chromosome Location	chr8:126614369-126614370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:126442074..126444761-chr8:126614097..126617217,3	MCF-7	breast:
2	chr8:126612687..126615177-chr8:126616929..126619166,2	MCF-7	breast:
3	chr8:126441405..126444224-chr8:126614301..126619460,8	MCF-7	breast:
4	chr8:126612725..126615017-chr8:126618565..126620143,2	MCF-7	breast:
5	chr8:126610481..126612816-chr8:126612922..126614971,2	MCF-7	breast:
6	chr8:126520498..126522119-chr8:126613658..126615873,2	MCF-7	breast:
7	chr8:126605005..126607033-chr8:126613419..126615572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1006998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17323382	0.89[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs17330350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17330462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085125	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs55752928	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56112519	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56262214	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60426038	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62521562	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470368	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6981191	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7017624	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7017801	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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
rs10956253	ZNF572	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126606800-126614800	Weak transcription	Osteobl	bone
2	chr8:126607800-126614600	Weak transcription	A549	lung
3	chr8:126608400-126618400	Weak transcription	Colonic Mucosa	Colon
4	chr8:126608600-126619800	Weak transcription	Small Intestine	intestine
5	chr8:126608800-126617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr8:126609600-126619800	Weak transcription	Esophagus	oesophagus
7	chr8:126611800-126622600	Enhancers	Primary B cells from peripheral blood	blood
8	chr8:126612200-126614800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:126612200-126625400	Enhancers	Primary B cells from cord blood	blood
10	chr8:126612800-126614400	Enhancers	Spleen	Spleen
11	chr8:126612800-126615600	Weak transcription	Fetal Thymus	thymus
12	chr8:126613200-126614400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr8:126613200-126621800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr8:126613400-126614800	Enhancers	Placenta	Placenta
15	chr8:126613400-126615000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr8:126613400-126615400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr8:126613400-126619000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:126613600-126615000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr8:126613600-126620600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:126613600-126620800	Enhancers	HMEC	breast
21	chr8:126613600-126621000	Enhancers	NHEK	skin
22	chr8:126613800-126614400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr8:126613800-126614400	Flanking Active TSS	GM12878-XiMat	blood
24	chr8:126613800-126615000	Weak transcription	NHDF-Ad	bronchial
25	chr8:126613800-126618600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr8:126613800-126621000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:126614000-126614400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr8:126614000-126614400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:126614000-126614400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:126614000-126614400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr8:126614000-126615600	Enhancers	Hela-S3	cervix
32	chr8:126614000-126617000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:126614200-126614600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr8:126614200-126615600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr8:126614200-126620000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links