Variant report

Variant	rs13272076
Chromosome Location	chr8:61188832-61188833
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61185501..61190567-chr8:61191860..61196819,8	MCF-7	breast:
2	chr8:61188816..61193463-chr8:61245871..61250410,5	K562	blood:

Variant related genes	Relation type
ENSG00000178538	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10086341	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10093008	0.90[AFR][1000 genomes]
rs10097537	0.90[AFR][1000 genomes]
rs10101374	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957128	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11774698	0.87[AFR][1000 genomes]
rs11774872	0.88[AFR][1000 genomes]
rs11781514	0.87[AFR][1000 genomes]
rs11994317	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266513	0.86[AFR][1000 genomes]
rs13267008	0.90[AFR][1000 genomes]
rs13269948	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1480339	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1824999	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1904780	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737556	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471856	0.86[AFR][1000 genomes]
rs6471857	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6471858	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6471859	0.90[AFR][1000 genomes]
rs6471860	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983830	0.90[AFR][1000 genomes]
rs6998446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001157	0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7002077	0.80[AFR][1000 genomes]
rs7002369	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7002846	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7002871	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7004004	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463930	0.88[AFR][1000 genomes]
rs7463939	0.90[AFR][1000 genomes]
rs7464181	0.92[AFR][1000 genomes]
rs7464531	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813357	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7825247	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7826329	0.88[AFR][1000 genomes]
rs7832419	0.90[AFR][1000 genomes]
rs7840279	0.90[AFR][1000 genomes]
rs7841396	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845524	0.90[AFR][1000 genomes]
rs8180936	0.87[YRI][hapmap]
rs9643367	0.89[YRI][hapmap]
rs9643368	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv831333	chr8:61102862-61275122	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv890943	chr8:61134995-61225652	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13272076	CA8	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61167000-61193200	Weak transcription	Gastric	stomach
2	chr8:61167000-61193200	Weak transcription	Lung	lung
3	chr8:61167000-61193200	Weak transcription	Pancreas	Pancrea
4	chr8:61172800-61191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:61178000-61191000	Weak transcription	Fetal Stomach	stomach
6	chr8:61179800-61191000	Weak transcription	Fetal Intestine Small	intestine
7	chr8:61184800-61190400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr8:61185200-61189000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:61186200-61190800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:61187000-61189000	Strong transcription	Fetal Intestine Large	intestine
11	chr8:61187200-61193000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:61187200-61193000	Weak transcription	Brain Anterior Caudate	brain
13	chr8:61187600-61189000	Genic enhancers	K562	blood
14	chr8:61187600-61192800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr8:61187800-61189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr8:61187800-61193000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:61187800-61193200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr8:61188200-61189000	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links