Variant report

Variant	rs1676029
Chromosome Location	chr6:106996452-106996453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106937771..106940207-chr6:106996030..106997572,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1676007	0.93[AMR][1000 genomes]
rs1676009	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1676011	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1676012	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1676013	0.85[AMR][1000 genomes]
rs1676014	0.93[AMR][1000 genomes]
rs1676015	0.93[AMR][1000 genomes]
rs1676030	0.85[YRI][hapmap]
rs1770724	0.86[AMR][1000 genomes]
rs1770725	0.86[AMR][1000 genomes]
rs1770727	0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1770729	0.93[AMR][1000 genomes]
rs1770730	0.93[AMR][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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
3	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
5	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
7	chr6:106988200-107001400	Weak transcription	Lung	lung
8	chr6:106991200-106999600	Strong transcription	Dnd41	blood
9	chr6:106992600-106996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:106993200-106996600	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:106993600-106998400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:106993800-106996600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:106993800-106996600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:106993800-106996600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:106993800-106996600	Enhancers	NH-A	brain
16	chr6:106994000-106996600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:106994000-106996600	Enhancers	HepG2	liver
18	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:106994200-106997000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:106994200-107000200	Weak transcription	Esophagus	oesophagus
21	chr6:106994200-107009000	Weak transcription	Left Ventricle	heart
22	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr6:106994400-106996600	Enhancers	Fetal Thymus	thymus
25	chr6:106994400-107000800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:106994600-106996600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:106994600-106996600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:106994600-106996600	Enhancers	Fetal Intestine Large	intestine
29	chr6:106994600-106996600	Enhancers	NHDF-Ad	bronchial
30	chr6:106994600-106997000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:106994600-106999600	Strong transcription	GM12878-XiMat	blood
32	chr6:106994600-107001400	Weak transcription	Spleen	Spleen
33	chr6:106994800-106996600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:106994800-106996600	Enhancers	Fetal Intestine Small	intestine
35	chr6:106994800-107000800	Weak transcription	Liver	Liver
36	chr6:106994800-107004200	Strong transcription	Primary T cells from cord blood	blood
37	chr6:106994800-107004600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:106994800-107004600	Weak transcription	Hela-S3	cervix
39	chr6:106995000-106996600	Enhancers	HUVEC	blood vessel
40	chr6:106995000-106996600	Flanking Active TSS	NHEK	skin
41	chr6:106995000-106999200	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr6:106995000-106999200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr6:106995000-107019400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:106995200-106996600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr6:106995200-106996800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:106995200-106997000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:106995200-106997000	Enhancers	HMEC	breast
48	chr6:106995200-107002000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:106995200-107016200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:106995200-107018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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