Variant report

Variant	rs62391627
Chromosome Location	chr6:1930891-1930892
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1609450..1612431-chr6:1929248..1931252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10900914	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969985	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528819	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12530211	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664587	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570537	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17134549	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17134557	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2628442	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2628443	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2628445	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2628455	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2761233	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2761235	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800136	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4512269	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56031192	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56226194	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390680	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62390682	0.81[EUR][1000 genomes]
rs62391624	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62391626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391628	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62391632	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914444	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916130	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72841994	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7759192	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759496	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
2	chr6:1905400-1962000	Weak transcription	Pancreas	Pancrea
3	chr6:1908400-1933600	Weak transcription	Liver	Liver
4	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
5	chr6:1915200-1934000	Weak transcription	Left Ventricle	heart
6	chr6:1915200-1937600	Weak transcription	Esophagus	oesophagus
7	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
8	chr6:1916000-1960800	Weak transcription	Gastric	stomach
9	chr6:1916600-1935000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:1918000-1933600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:1918600-1933400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:1918600-1946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:1918600-1957800	Weak transcription	Dnd41	blood
14	chr6:1919000-1933000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:1919200-1934400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:1919600-1962400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:1920200-1932000	Weak transcription	Primary B cells from cord blood	blood
18	chr6:1920400-1933200	Weak transcription	GM12878-XiMat	blood
19	chr6:1921600-1931000	Weak transcription	Fetal Kidney	kidney
20	chr6:1922400-1934800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:1924000-1952800	Weak transcription	Fetal Stomach	stomach
22	chr6:1924400-1941800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:1926800-1932000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:1927800-1933400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:1928000-1932200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:1928000-1933600	Weak transcription	Primary T cells from cord blood	blood
27	chr6:1928000-1936400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:1928200-1933200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:1928200-1940800	Weak transcription	Hela-S3	cervix
30	chr6:1928800-1938800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:1929200-1935000	Weak transcription	Fetal Intestine Small	intestine
32	chr6:1929400-1932400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:1929600-1931200	Enhancers	Brain Germinal Matrix	brain
34	chr6:1929600-1933200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:1929800-1934400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:1930000-1931400	Enhancers	Fetal Lung	lung
37	chr6:1930200-1931000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:1930200-1931200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:1930400-1931200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:1930400-1943400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:1930600-1931000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:1930600-1936400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:1930600-1936600	Weak transcription	Aorta	Aorta
44	chr6:1930600-1952600	Weak transcription	Fetal Intestine Large	intestine
45	chr6:1930800-1931000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:1930800-1932000	Weak transcription	HepG2	liver

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