Variant report

Variant	rs12525799
Chromosome Location	chr6:80332105-80332106
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1033535	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12526427	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12526644	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527512	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530052	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17505891	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1883879	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2655684	0.81[CHD][hapmap]
rs34532743	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812155	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812159	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649340	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55781748	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72905738	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72905744	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72905757	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv886304	chr6:80294265-80355973	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80315000-80340600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:80318000-80340200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:80320800-80338600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:80322600-80340000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:80322800-80340400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:80326600-80338200	Weak transcription	Stomach Mucosa	stomach
7	chr6:80326600-80339000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:80331400-80332400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:80331600-80333200	Enhancers	Fetal Intestine Large	intestine
10	chr6:80331600-80333400	Enhancers	HepG2	liver
11	chr6:80331600-80333400	Enhancers	K562	blood
12	chr6:80331800-80332400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:80331800-80333400	Enhancers	Fetal Intestine Small	intestine
14	chr6:80331800-80338200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:80332000-80332200	Enhancers	Duodenum Mucosa	Duodenum
16	chr6:80332000-80332400	Enhancers	Liver	Liver

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links