Variant report

Variant	rs12664553
Chromosome Location	chr6:139904892-139904893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:139773028..139775843-chr6:139903683..139906144,2	K562	blood:
2	chr6:139691841..139699576-chr6:139900868..139917289,34	MCF-7	breast:
3	chr6:139904154..139906110-chr6:139909809..139911631,3	K562	blood:
4	chr6:139904227..139905139-chr6:140201272..140201808,2	MCF-7	breast:
5	chr6:139904084..139907083-chr6:139974866..139976418,2	K562	blood:
6	chr6:139691228..139697226-chr6:139904818..139909765,9	K562	blood:
7	chr6:139902793..139905980-chr6:139905991..139910426,4	MCF-7	breast:
8	chr6:139892341..139894694-chr6:139904395..139906288,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11751645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660850	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17069030	0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4896477	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs61117481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73775562	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9321729	0.89[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	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv970368	chr6:139903788-139911187	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12664553	NGF	trans	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139899000-139907000	Weak transcription	K562	blood
2	chr6:139899600-139908800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:139900000-139907400	Weak transcription	Pancreas	Pancrea
4	chr6:139900000-139908800	Weak transcription	Fetal Lung	lung
5	chr6:139900200-139909000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:139900400-139908800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:139900400-139908800	Weak transcription	Fetal Intestine Large	intestine
8	chr6:139900800-139908800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:139900800-139919200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:139902400-139906800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:139902400-139909200	Weak transcription	Right Ventricle	heart
12	chr6:139902600-139906800	Weak transcription	Fetal Kidney	kidney
13	chr6:139902600-139907200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:139902600-139908000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:139903200-139906200	Enhancers	Placenta	Placenta
16	chr6:139903600-139905000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:139903800-139905000	Enhancers	NH-A	brain
18	chr6:139903800-139905600	Enhancers	A549	lung
19	chr6:139904000-139905000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:139904000-139905000	Enhancers	NHEK	skin
21	chr6:139904000-139905000	Enhancers	NHLF	lung
22	chr6:139904000-139905000	Enhancers	Osteobl	bone
23	chr6:139904200-139905000	Enhancers	HMEC	breast
24	chr6:139904200-139905400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:139904400-139905600	Enhancers	HepG2	liver
26	chr6:139904400-139906200	Enhancers	HUVEC	blood vessel
27	chr6:139904400-139907000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:139904400-139907200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:139904600-139905000	Enhancers	Fetal Heart	heart
30	chr6:139904600-139908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:139904800-139907600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:139904800-139907600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:139904800-139907600	Weak transcription	Hela-S3	cervix
34	chr6:139904800-139908200	Weak transcription	HSMM	muscle
35	chr6:139904800-139908200	Weak transcription	NHDF-Ad	bronchial
36	chr6:139904800-139908800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:139904800-139908800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:139904800-139908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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