Variant report

Variant	rs61223539
Chromosome Location	chr1:85931843-85931844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85929292-85931998	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:85928502-85932579	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:85931475-85931918	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:85929750-85931907	ProgFib	skin:	n/a	n/a
5	POLR2A	chr1:85928236-85932598	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:85928257-85932490	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:85928095-85932547	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:85928913-85932472	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:85929625-85931965	IMR90	lung:	n/a	n/a
10	POLR2A	chr1:85929268-85932094	PANC-1	pancreas:	n/a	n/a
11	USF2	chr1:85931662-85931844	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:85928110-85932105	PANC-1	pancreas:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85744913..85746846-chr1:85930995..85932650,2	MCF-7	breast:
2	chr1:85929364..85932220-chr1:86042357..86044099,2	MCF-7	breast:
3	chr1:85931146..85932726-chr1:86032446..86035420,2	MCF-7	breast:
4	chr1:85930091..85932037-chr1:86045511..86048058,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000273264	TF binding region
DDAH1	TF binding region
ENSG00000153904	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1241320	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13373844	0.87[ASN][1000 genomes]
rs17388780	0.87[ASN][1000 genomes]
rs17389112	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36104818	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs527762	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs529582	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs597168	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61783057	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555486	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3437564	chr1:85929789-85932337	Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85931000-85932000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:85931000-85932000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:85931000-85932000	Flanking Active TSS	NH-A	brain
4	chr1:85931000-85932200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:85931200-85932000	Flanking Active TSS	HUVEC	blood vessel
6	chr1:85931200-85932000	Flanking Active TSS	Osteobl	bone
7	chr1:85931200-85941600	Weak transcription	Aorta	Aorta
8	chr1:85931200-85942200	Weak transcription	Esophagus	oesophagus
9	chr1:85931400-85932000	Enhancers	Pancreas	Pancrea
10	chr1:85931400-85932000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:85931400-85932000	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:85931400-85932000	Flanking Active TSS	NHDF-Ad	bronchial
13	chr1:85931600-85932000	Enhancers	Liver	Liver
14	chr1:85931600-85932000	Enhancers	Fetal Intestine Large	intestine
15	chr1:85931600-85932000	Enhancers	Fetal Stomach	stomach
16	chr1:85931600-85932200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:85931800-85932000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:85931800-85932000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:85931800-85932000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:85931800-85932000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:85931800-85932000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:85931800-85932000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:85931800-85932000	Enhancers	Fetal Intestine Small	intestine
24	chr1:85931800-85932000	Enhancers	HepG2	liver
25	chr1:85931800-85932400	Enhancers	HSMM	muscle
26	chr1:85931800-85933600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:85931800-85938800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:85931800-85938800	Weak transcription	HSMMtube	muscle
29	chr1:85931800-85942400	Weak transcription	NHLF	lung
30	chr1:85931800-85956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:85931800-85960000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links