Variant report

Variant	rs71662160
Chromosome Location	chr1:86885562-86885563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:86885507-86885593	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:86884770..86885617-chr1:86965291..86966347,4	K562	blood:
2	chr1:86885110..86885636-chr1:86939415..86940377,2	K562	blood:
3	chr1:86885099..86885732-chr1:86973485..86974031,3	MCF-7	breast:
4	chr1:86884690..86885606-chr1:86967410..86968457,3	K562	blood:
5	chr1:86884671..86885639-chr1:86965279..86966251,3	MCF-7	breast:
6	chr1:86884967..86885568-chr1:86965463..86966341,2	MCF-7	breast:

No data

Variant related genes	Relation type
CLCA2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12724057	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12733468	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12741127	0.81[AFR][1000 genomes]
rs12749637	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12757699	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12758659	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1334139	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17129145	1.00[AMR][1000 genomes]
rs17129150	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17129169	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17129194	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34204564	0.82[AFR][1000 genomes]
rs34495136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34513089	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34536842	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34834083	0.83[AMR][1000 genomes]
rs34851039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35261823	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35303211	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35408727	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35604082	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35908397	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35950578	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36036063	0.83[AFR][1000 genomes]
rs4592241	0.81[AFR][1000 genomes]
rs55917045	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71662157	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs71662158	0.82[AMR][1000 genomes]
rs71662161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs932692	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	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	chr1:86882200-86894800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:86885000-86885600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:86885000-86889200	Enhancers	NHEK	skin
4	chr1:86885200-86885600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86885200-86885600	Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:86885200-86885800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:86885200-86886000	Enhancers	Fetal Heart	heart
8	chr1:86885200-86886600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:86885200-86887200	Enhancers	Hela-S3	cervix
10	chr1:86885200-86889400	Enhancers	HMEC	breast
11	chr1:86885200-86889600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:86885400-86885800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:86885400-86886800	Weak transcription	NHDF-Ad	bronchial
14	chr1:86885400-86887200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:86885400-86887400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:86885400-86887800	Weak transcription	Esophagus	oesophagus

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