Variant report

Variant	rs61164145
Chromosome Location	chr1:85924252-85924253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85921195..85924566-chr1:85929657..85932092,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12021849	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022443	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022538	0.92[EUR][1000 genomes]
rs12023795	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024508	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029684	0.84[EUR][1000 genomes]
rs12033315	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	0.84[EUR][1000 genomes]
rs12038279	0.92[EUR][1000 genomes]
rs12043604	0.84[EUR][1000 genomes]
rs12047139	0.92[EUR][1000 genomes]
rs12049582	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1851782	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	0.84[EUR][1000 genomes]
rs485987	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85914200-85924800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:85915600-85925400	Weak transcription	Brain Germinal Matrix	brain
4	chr1:85917400-85926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:85917400-85929400	Weak transcription	Gastric	stomach
7	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
8	chr1:85917800-85927200	Weak transcription	NH-A	brain
9	chr1:85917800-85928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:85919200-85928400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:85919400-85924800	Weak transcription	Fetal Kidney	kidney
12	chr1:85919400-85927200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:85919600-85928200	Weak transcription	Fetal Brain Female	brain
14	chr1:85919800-85925000	Weak transcription	Adipose Nuclei	Adipose
15	chr1:85920000-85924800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:85920000-85925000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:85920000-85925000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:85920000-85929600	Weak transcription	Brain Substantia Nigra	brain
19	chr1:85920200-85925000	Weak transcription	Aorta	Aorta
20	chr1:85920200-85925400	Weak transcription	Ovary	ovary
21	chr1:85920200-85926400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:85920200-85928000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:85920400-85926400	Weak transcription	NHLF	lung
24	chr1:85920600-85924800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:85920600-85925000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:85920800-85925000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:85920800-85929000	Weak transcription	HSMMtube	muscle
28	chr1:85921600-85925000	Weak transcription	NHDF-Ad	bronchial
29	chr1:85922000-85924600	Weak transcription	HUVEC	blood vessel
30	chr1:85922000-85925000	Weak transcription	Fetal Brain Male	brain
31	chr1:85922200-85925400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:85922600-85928400	Enhancers	Fetal Intestine Large	intestine
33	chr1:85922600-85929000	Enhancers	Fetal Intestine Small	intestine
34	chr1:85923200-85925800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:85923200-85926200	Enhancers	Stomach Mucosa	stomach
36	chr1:85923200-85927000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:85923200-85929800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:85923400-85925400	Enhancers	Fetal Stomach	stomach
39	chr1:85923600-85925000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:85923600-85927000	Enhancers	HepG2	liver
41	chr1:85923600-85928200	Enhancers	Liver	Liver
42	chr1:85923800-85925800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:85923800-85926200	Enhancers	Rectal Smooth Muscle	rectum
44	chr1:85924000-85925000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:85924000-85925800	Weak transcription	HSMM	muscle
46	chr1:85924000-85925800	Weak transcription	Osteobl	bone
47	chr1:85924000-85926000	Enhancers	Fetal Lung	lung
48	chr1:85924200-85924400	Enhancers	Pancreas	Pancrea
49	chr1:85924200-85925400	Enhancers	Small Intestine	intestine
50	chr1:85924200-85926800	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links