Variant report

Variant	rs12564057
Chromosome Location	chr1:86076709-86076710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86046521..86048351-chr1:86075953..86079253,3	MCF-7	breast:
2	chr1:86041793..86044827-chr1:86073934..86077302,3	K562	blood:
3	chr1:86064019..86065868-chr1:86075742..86078671,2	K562	blood:
4	chr1:86073205..86075088-chr1:86076581..86078830,2	K562	blood:
5	chr1:86045659..86048173-chr1:86076180..86078969,3	MCF-7	breast:
6	chr1:86045439..86048632-chr1:86076708..86079652,4	K562	blood:
7	chr1:86042110..86043822-chr1:86074708..86077302,2	K562	blood:

Variant related genes	Relation type
ENSG00000230285	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12563476	1.00[AFR][1000 genomes]
rs12564468	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12565129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12566306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1360240	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17128012	0.84[ASN][1000 genomes]
rs17128152	1.00[AFR][1000 genomes]
rs17128155	1.00[AFR][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	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86048800-86081200	Weak transcription	Gastric	stomach
2	chr1:86066600-86077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:86070000-86076800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:86071200-86076800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:86071600-86078800	Enhancers	NHLF	lung
6	chr1:86071800-86076800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:86072200-86077600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:86073000-86078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:86073200-86076800	Weak transcription	Fetal Heart	heart
10	chr1:86073200-86077000	Weak transcription	Ovary	ovary
11	chr1:86073200-86078400	Weak transcription	Pancreas	Pancrea
12	chr1:86073200-86082200	Weak transcription	Aorta	Aorta
13	chr1:86073600-86076800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:86073600-86078000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:86073800-86077400	Weak transcription	HepG2	liver
16	chr1:86073800-86078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:86073800-86078600	Weak transcription	Hela-S3	cervix
18	chr1:86074000-86078400	Enhancers	A549	lung
19	chr1:86074200-86077400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:86074200-86077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:86074200-86078000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:86074200-86078400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:86074200-86078400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:86074200-86078400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:86074200-86081200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:86074400-86076800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:86074400-86076800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:86074400-86076800	Weak transcription	HMEC	breast
29	chr1:86074400-86077400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:86074400-86077400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:86074400-86077800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:86074400-86077800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:86074400-86078400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:86074600-86077200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:86074600-86077400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:86074600-86077600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:86074600-86077600	Weak transcription	HUVEC	blood vessel
38	chr1:86074800-86076800	Weak transcription	Fetal Intestine Large	intestine
39	chr1:86075200-86076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:86075400-86076800	Enhancers	HSMM	muscle
41	chr1:86076000-86077000	Enhancers	Osteobl	bone
42	chr1:86076200-86076800	Enhancers	HSMMtube	muscle
43	chr1:86076200-86077400	Weak transcription	Fetal Kidney	kidney
44	chr1:86076400-86076800	Enhancers	NH-A	brain
45	chr1:86076400-86077200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:86076400-86077400	Enhancers	NHEK	skin
47	chr1:86076600-86077000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:86076600-86077000	Flanking Active TSS	NHDF-Ad	bronchial
49	chr1:86076600-86077200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:86076600-86077800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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