Variant report

Variant	rs9399580
Chromosome Location	chr6:146878029-146878030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11155475	0.89[EUR][1000 genomes]
rs12189826	0.89[EUR][1000 genomes]
rs3804286	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804288	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804289	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570768	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6915941	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6918907	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6939108	0.84[EUR][1000 genomes]
rs7773384	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9373498	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9377003	0.88[EUR][1000 genomes]
rs9377004	0.89[EUR][1000 genomes]
rs9390393	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033913	chr6:146572989-147092365	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538466	chr6:146572989-147092365	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv886749	chr6:146679735-147123699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146865800-146878200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:146866400-146881800	Weak transcription	Brain Germinal Matrix	brain
3	chr6:146866600-146883800	Weak transcription	Small Intestine	intestine
4	chr6:146866600-146885800	Weak transcription	Pancreas	Pancrea
5	chr6:146867000-146880600	Weak transcription	Right Ventricle	heart
6	chr6:146872400-146878200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:146872800-146878200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:146873800-146878200	Weak transcription	Stomach Mucosa	stomach
9	chr6:146876000-146878200	Weak transcription	Hela-S3	cervix
10	chr6:146876400-146878200	Weak transcription	Left Ventricle	heart
11	chr6:146876400-146878400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:146876400-146883600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:146876400-146891400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:146876600-146878200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:146876600-146878200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:146876600-146878200	Weak transcription	Fetal Kidney	kidney
17	chr6:146876600-146878200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:146876600-146878200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:146876600-146878200	Weak transcription	HSMMtube	muscle
20	chr6:146876600-146878400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:146876600-146878400	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:146876600-146880600	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:146876600-146880800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:146876600-146881000	Weak transcription	HMEC	breast
25	chr6:146876600-146891200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:146876800-146878400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:146876800-146878400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:146876800-146878400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:146876800-146878400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:146876800-146878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:146876800-146878400	Weak transcription	Fetal Lung	lung
32	chr6:146876800-146878400	Weak transcription	Fetal Thymus	thymus
33	chr6:146876800-146878400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:146876800-146878400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:146876800-146878400	Weak transcription	HepG2	liver
36	chr6:146876800-146880000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:146876800-146880800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:146876800-146880800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:146876800-146880800	Weak transcription	Adipose Nuclei	Adipose
40	chr6:146876800-146880800	Weak transcription	Colonic Mucosa	Colon
41	chr6:146876800-146880800	Weak transcription	Fetal Intestine Large	intestine
42	chr6:146876800-146880800	Weak transcription	NH-A	brain
43	chr6:146876800-146880800	Weak transcription	NHLF	lung
44	chr6:146876800-146881000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:146876800-146881800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:146876800-146881800	Weak transcription	HUVEC	blood vessel
47	chr6:146876800-146882200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:146876800-146882200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:146876800-146882200	Weak transcription	Liver	Liver
50	chr6:146876800-146883600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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