Variant report

Variant	rs1676023
Chromosome Location	chr6:106993594-106993595
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	chr6:106982665..106985601-chr6:106993025..106995759,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1111830	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1613722	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1616375	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676008	0.86[ASN][1000 genomes]
rs1676010	0.86[ASN][1000 genomes]
rs1676024	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1676025	0.93[ASN][1000 genomes]
rs1676026	0.91[EUR][1000 genomes]
rs1676028	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1770718	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770719	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770720	0.91[EUR][1000 genomes]
rs1770721	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770722	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1770723	0.86[ASN][1000 genomes]
rs1770733	0.86[ASN][1000 genomes]
rs2066201	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247335	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615209	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3747789	0.82[ASN][1000 genomes]
rs6902745	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7771502	0.82[ASN][1000 genomes]
rs783395	0.82[ASN][1000 genomes]
rs783396	0.82[ASN][1000 genomes]
rs783401	0.82[ASN][1000 genomes]
rs9386565	0.82[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	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:73 , 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	chr6:106978800-106993800	Weak transcription	NHLF	lung
5	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
6	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
7	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:106985000-106993800	Weak transcription	NH-A	brain
9	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
10	chr6:106986200-106994000	Weak transcription	Stomach Mucosa	stomach
11	chr6:106986400-106994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:106986400-106995000	Weak transcription	Thymus	Thymus
13	chr6:106986800-106994400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:106987000-106993600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:106987400-106993800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr6:106987800-106993800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:106988200-106993800	Weak transcription	Esophagus	oesophagus
18	chr6:106988200-107001400	Weak transcription	Lung	lung
19	chr6:106988400-106994000	Strong transcription	GM12878-XiMat	blood
20	chr6:106988400-106995600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:106988800-106994600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:106989000-106994000	Strong transcription	Fetal Intestine Large	intestine
23	chr6:106989200-106994000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:106989200-106994600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:106989400-106993800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:106989800-106993800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:106989800-106994000	Weak transcription	Hela-S3	cervix
28	chr6:106989800-106995800	Weak transcription	Fetal Stomach	stomach
29	chr6:106991000-106993800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:106991000-106993800	Weak transcription	HSMM	muscle
31	chr6:106991200-106993600	Strong transcription	Fetal Thymus	thymus
32	chr6:106991200-106993800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:106991200-106994000	Strong transcription	Primary T cells from cord blood	blood
34	chr6:106991200-106994600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:106991200-106999600	Strong transcription	Dnd41	blood
36	chr6:106991400-106994800	Strong transcription	Liver	Liver
37	chr6:106992000-106993600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:106992000-106993800	Weak transcription	Spleen	Spleen
39	chr6:106992000-106994800	Weak transcription	Fetal Intestine Small	intestine
40	chr6:106992000-106995400	Weak transcription	Colon Smooth Muscle	Colon
41	chr6:106992600-106996400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:106992600-106996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:106992800-106993600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:106992800-106993600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:106992800-106994400	Genic enhancers	Primary B cells from cord blood	blood
46	chr6:106992800-106995800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:106993000-106993600	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:106993000-106993800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:106993000-106994000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:106993000-106994000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links