Variant report

Variant	rs2629472
Chromosome Location	chr6:80174658-80174659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:79942688..79944316-chr6:80174273..80176094,2	MCF-7	breast:
2	chr6:79784565..79790401-chr6:80174482..80177325,6	MCF-7	breast:
3	chr6:79786335..79788138-chr6:80172586..80175202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270362	Chromatin interaction
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10498921	0.81[EUR][1000 genomes]
rs1158770	0.99[EUR][1000 genomes]
rs1158771	0.99[EUR][1000 genomes]
rs11965020	0.86[EUR][1000 genomes]
rs11966497	0.81[EUR][1000 genomes]
rs1385536	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385537	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1485370	0.99[EUR][1000 genomes]
rs1485372	0.98[EUR][1000 genomes]
rs1485377	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16890774	0.98[EUR][1000 genomes]
rs16890835	0.82[EUR][1000 genomes]
rs16890850	0.81[EUR][1000 genomes]
rs17727505	0.98[EUR][1000 genomes]
rs2437702	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2575204	0.99[EUR][1000 genomes]
rs2575208	0.87[EUR][1000 genomes]
rs2629473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655666	0.90[EUR][1000 genomes]
rs2655677	0.87[EUR][1000 genomes]
rs2655680	0.87[EUR][1000 genomes]
rs2655703	0.86[EUR][1000 genomes]
rs2803188	0.88[EUR][1000 genomes]
rs2803197	0.84[EUR][1000 genomes]
rs41269343	0.87[EUR][1000 genomes]
rs55989614	0.81[EUR][1000 genomes]
rs62411324	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411332	0.87[EUR][1000 genomes]
rs62411348	0.86[EUR][1000 genomes]
rs62413360	0.84[EUR][1000 genomes]
rs62413366	0.82[EUR][1000 genomes]
rs62413368	0.81[EUR][1000 genomes]
rs62413370	0.82[EUR][1000 genomes]
rs62413371	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62413372	0.81[EUR][1000 genomes]
rs62413377	0.81[EUR][1000 genomes]
rs62413380	0.80[EUR][1000 genomes]
rs6454124	0.80[EUR][1000 genomes]
rs6454125	0.80[EUR][1000 genomes]
rs7763268	0.80[EUR][1000 genomes]
rs7767034	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768724	0.80[EUR][1000 genomes]
rs7775232	0.81[EUR][1000 genomes]
rs992872	0.90[EUR][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	nsv1030126	chr6:80113449-80209165	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	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
6	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	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
8	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80171200-80176200	Weak transcription	Adipose Nuclei	Adipose
2	chr6:80171200-80220000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:80171600-80175800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:80171600-80226600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:80173200-80175400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:80173200-80175800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:80173200-80175800	Enhancers	Hela-S3	cervix
8	chr6:80173200-80179600	Enhancers	HepG2	liver
9	chr6:80173400-80175000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:80173600-80177200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:80173600-80177400	Weak transcription	Placenta	Placenta
12	chr6:80173800-80175000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:80173800-80175000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:80173800-80175000	Weak transcription	HUVEC	blood vessel
15	chr6:80173800-80175200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:80174000-80175000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:80174000-80177600	Weak transcription	NHEK	skin
18	chr6:80174000-80191800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:80174200-80175200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:80174200-80177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:80174200-80177800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:80174400-80175200	Weak transcription	Fetal Intestine Large	intestine

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