Variant report

Variant	rs56216312
Chromosome Location	chr1:85918454-85918455
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	chr1:85913232..85915386-chr1:85917552..85919124,2	K562	blood:
2	chr1:85917225..85920485-chr1:85926526..85929082,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11582061	0.92[EUR][1000 genomes]
rs11588128	0.86[EUR][1000 genomes]
rs12564550	0.89[EUR][1000 genomes]
rs12564698	0.87[EUR][1000 genomes]
rs12568573	0.86[EUR][1000 genomes]
rs12568675	0.85[EUR][1000 genomes]
rs17127199	0.89[EUR][1000 genomes]
rs2935	0.99[EUR][1000 genomes]
rs3813600	1.00[AFR][1000 genomes]
rs55639236	0.88[EUR][1000 genomes]
rs56154783	0.85[EUR][1000 genomes]
rs56215900	0.89[EUR][1000 genomes]
rs6658151	0.84[EUR][1000 genomes]
rs67644506	0.99[EUR][1000 genomes]
rs72722664	1.00[AFR][1000 genomes]
rs72724632	0.89[EUR][1000 genomes]
rs7540169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85907000-85919600	Weak transcription	Right Atrium	heart
3	chr1:85913800-85920400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:85914200-85924800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:85914400-85918800	Weak transcription	HepG2	liver
6	chr1:85915000-85919200	Weak transcription	HSMMtube	muscle
7	chr1:85915200-85918600	Weak transcription	Fetal Stomach	stomach
8	chr1:85915200-85918600	Weak transcription	Ovary	ovary
9	chr1:85915200-85918800	Weak transcription	Adipose Nuclei	Adipose
10	chr1:85915200-85919600	Weak transcription	Aorta	Aorta
11	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:85915400-85918800	Weak transcription	Fetal Brain Female	brain
13	chr1:85915400-85919000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:85915400-85919000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:85915400-85919200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:85915400-85919400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:85915600-85919000	Weak transcription	NHLF	lung
18	chr1:85915600-85919200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:85915600-85920200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:85915600-85925400	Weak transcription	Brain Germinal Matrix	brain
21	chr1:85915800-85920600	Weak transcription	Small Intestine	intestine
22	chr1:85916400-85919000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:85916400-85920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:85916400-85921800	Enhancers	Liver	Liver
25	chr1:85916600-85918800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:85916600-85920000	Genic enhancers	Osteobl	bone
27	chr1:85916800-85918600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:85916800-85919200	Enhancers	Brain Anterior Caudate	brain
29	chr1:85917000-85922200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:85917000-85923000	Weak transcription	Psoas Muscle	Psoas
31	chr1:85917200-85918600	Weak transcription	NHDF-Ad	bronchial
32	chr1:85917200-85920000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:85917400-85918600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:85917400-85918600	Strong transcription	HSMM	muscle
35	chr1:85917400-85919000	Weak transcription	Pancreas	Pancrea
36	chr1:85917400-85919000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:85917400-85919400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:85917400-85919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:85917400-85919600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:85917400-85919600	Weak transcription	Lung	lung
41	chr1:85917400-85919600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:85917400-85920000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:85917400-85922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:85917400-85926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:85917400-85929400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:85917400-85929400	Weak transcription	Gastric	stomach
47	chr1:85917400-85929800	Weak transcription	Esophagus	oesophagus
48	chr1:85917600-85921600	Enhancers	Fetal Lung	lung
49	chr1:85917800-85918800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:85917800-85919000	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links