Variant report

Variant	rs12528284
Chromosome Location	chr6:167013993-167013994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12661452	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2032544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2032545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34324183	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35574615	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35798186	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3778379	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3778380	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3778381	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3778383	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3799578	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799590	0.88[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3799591	0.88[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3799592	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3799593	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3799594	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3799595	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3799596	0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3799599	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3799601	0.89[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3823196	0.88[CEU][hapmap];0.89[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3823197	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6907098	0.89[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6907443	0.89[CHB][hapmap];0.91[EUR][1000 genomes]
rs9295356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9347138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9348149	0.89[CHB][hapmap];0.91[EUR][1000 genomes]
rs9355586	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9356491	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9356493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9356494	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366031	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9366033	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167009400-167015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:167009600-167014200	Weak transcription	HMEC	breast
3	chr6:167009600-167014800	Enhancers	NH-A	brain
4	chr6:167010200-167014000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:167010200-167014000	Enhancers	Lung	lung
6	chr6:167010600-167014000	Enhancers	Left Ventricle	heart
7	chr6:167010800-167014000	Enhancers	Adipose Nuclei	Adipose
8	chr6:167011000-167016800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:167011000-167021000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:167011400-167014000	Enhancers	Brain Anterior Caudate	brain
11	chr6:167011400-167014000	Enhancers	Brain Substantia Nigra	brain
12	chr6:167012000-167023600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:167012200-167014000	Enhancers	Brain Hippocampus Middle	brain
14	chr6:167012200-167014400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:167012200-167023400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:167012400-167014000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:167012400-167015600	Weak transcription	Aorta	Aorta
18	chr6:167012400-167025000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:167012400-167034400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:167012600-167015000	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr6:167012600-167015600	Weak transcription	Ovary	ovary
22	chr6:167012600-167016400	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:167012600-167025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:167012600-167027600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:167012800-167014600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:167012800-167015000	Enhancers	HUVEC	blood vessel
27	chr6:167012800-167015000	Enhancers	Osteobl	bone
28	chr6:167012800-167016200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:167012800-167016600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:167012800-167027800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:167013000-167014000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:167013000-167014000	Enhancers	Pancreas	Pancrea
33	chr6:167013000-167014000	Enhancers	Right Atrium	heart
34	chr6:167013000-167014000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:167013000-167014200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr6:167013000-167014400	Weak transcription	NHDF-Ad	bronchial
37	chr6:167013000-167015200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:167013200-167014000	Enhancers	Gastric	stomach
39	chr6:167013200-167014000	Enhancers	Psoas Muscle	Psoas
40	chr6:167013200-167016400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:167013200-167031000	Weak transcription	Fetal Intestine Small	intestine
42	chr6:167013400-167014000	Genic enhancers	NHLF	lung
43	chr6:167013400-167014400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:167013400-167014400	Enhancers	HSMM	muscle
45	chr6:167013400-167015600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:167013400-167016400	Weak transcription	Brain Germinal Matrix	brain
47	chr6:167013400-167028800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:167013600-167014200	Enhancers	Stomach Mucosa	stomach
49	chr6:167013600-167014600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:167013600-167015600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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