Variant report

Variant	rs3799673
Chromosome Location	chr6:166857657-166857658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166846709..166849612-chr6:166857165..166859206,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs2235288	0.91[EUR][1000 genomes]
rs2281057	1.00[EUR][1000 genomes]
rs2281058	1.00[EUR][1000 genomes]
rs2281059	1.00[EUR][1000 genomes]
rs2281060	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281061	1.00[EUR][1000 genomes]
rs2281062	0.93[EUR][1000 genomes]
rs2294327	0.83[EUR][1000 genomes]
rs2294328	0.83[EUR][1000 genomes]
rs4709113	1.00[EUR][1000 genomes]
rs6456083	1.00[EUR][1000 genomes]
rs73790206	1.00[EUR][1000 genomes]
rs7756092	1.00[EUR][1000 genomes]
rs9457169	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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	nsv886937	chr6:166830696-166922813	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166808200-166911800	Weak transcription	Psoas Muscle	Psoas
2	chr6:166824000-166901400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:166825200-166875800	Weak transcription	Colonic Mucosa	Colon
4	chr6:166827000-166873400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:166827600-166867200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:166830000-166866600	Weak transcription	Fetal Intestine Large	intestine
7	chr6:166833200-166864400	Weak transcription	Fetal Kidney	kidney
8	chr6:166833200-166879000	Weak transcription	NH-A	brain
9	chr6:166833400-166879000	Weak transcription	HSMM	muscle
10	chr6:166833600-166859600	Weak transcription	HMEC	breast
11	chr6:166834000-166866400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:166834200-166863800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:166834200-166879400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:166834600-166862000	Weak transcription	NHDF-Ad	bronchial
15	chr6:166838200-166860400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:166843000-166865200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:166844200-166860400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:166844200-166865200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:166845800-166860000	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:166845800-166860200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:166845800-166862000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:166845800-166863400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:166846000-166859200	Weak transcription	Osteobl	bone
24	chr6:166846000-166860600	Weak transcription	Liver	Liver
25	chr6:166846000-166861000	Weak transcription	HSMMtube	muscle
26	chr6:166846000-166861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:166846000-166862200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:166846000-166863200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:166846000-166881000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:166846200-166858000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:166846200-166859400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:166846200-166860400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:166847000-166858200	Weak transcription	NHLF	lung
34	chr6:166847000-166858600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:166847000-166858800	Weak transcription	Ovary	ovary
36	chr6:166847000-166859200	Weak transcription	Aorta	Aorta
37	chr6:166847800-166859400	Enhancers	Fetal Thymus	thymus
38	chr6:166848800-166865200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:166849400-166861000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:166850200-166859400	Weak transcription	Esophagus	oesophagus
41	chr6:166850200-166862000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:166850200-166863400	Weak transcription	Stomach Mucosa	stomach
43	chr6:166850200-166865200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:166850200-166870000	Weak transcription	Right Atrium	heart
45	chr6:166850400-166862000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:166851000-166858200	Enhancers	Thymus	Thymus
47	chr6:166851600-166858000	Weak transcription	Gastric	stomach
48	chr6:166851600-166860600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:166852000-166860000	Weak transcription	Brain Germinal Matrix	brain
50	chr6:166853400-166860200	Weak transcription	Spleen	Spleen

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