Variant report

Variant	rs9405533
Chromosome Location	chr6:1949812-1949813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1948965..1951899-chr6:1951907..1953697,2	MCF-7	breast:
2	chr6:1608996..1611183-chr6:1948987..1951585,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf195-30	chr6:1949489-1949978	NONHSAT106570

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12173320	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12175531	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1323631	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1802	1.00[YRI][hapmap]
rs2146920	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3800130	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3927456	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4959164	1.00[YRI][hapmap]
rs6900111	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6939971	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9405154	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9405155	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9405545	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
7	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
8	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
9	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:51 , 50 per page) page: 1 2

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	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
4	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
5	chr6:1916000-1960800	Weak transcription	Gastric	stomach
6	chr6:1918600-1957800	Weak transcription	Dnd41	blood
7	chr6:1919600-1962400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:1924000-1952800	Weak transcription	Fetal Stomach	stomach
9	chr6:1930600-1952600	Weak transcription	Fetal Intestine Large	intestine
10	chr6:1935200-1952200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:1935200-1953800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:1935400-1953000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:1935800-1964200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:1936400-1960000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:1936800-1958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:1937400-1961400	Weak transcription	Stomach Mucosa	stomach
17	chr6:1938200-1958400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:1940800-1967200	Weak transcription	Primary B cells from cord blood	blood
19	chr6:1940800-1969800	Weak transcription	Lung	lung
20	chr6:1941000-1952600	Weak transcription	Hela-S3	cervix
21	chr6:1941400-1958400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:1942200-1952800	Weak transcription	Aorta	Aorta
23	chr6:1942400-1960800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:1943600-1952000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:1943600-1966000	Weak transcription	GM12878-XiMat	blood
26	chr6:1944400-1964000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:1945600-1961600	Strong transcription	HepG2	liver
28	chr6:1946000-1961000	Weak transcription	Left Ventricle	heart
29	chr6:1946000-1964000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:1946400-1953400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr6:1947200-1952600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:1947400-1952600	Weak transcription	NHEK	skin
33	chr6:1947400-1980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:1947800-1956000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:1949000-1950000	Enhancers	Adipose Nuclei	Adipose
36	chr6:1949000-1950600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:1949000-1951200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr6:1949000-1958600	Weak transcription	Esophagus	oesophagus
39	chr6:1949400-1950000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:1949400-1950000	Enhancers	HMEC	breast
41	chr6:1949400-1950200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:1949400-1950200	Enhancers	Brain Substantia Nigra	brain
43	chr6:1949400-1950200	Enhancers	Osteobl	bone
44	chr6:1949400-1950800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr6:1949600-1950200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:1949600-1950400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:1949800-1950000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:1949800-1950000	Enhancers	Brain Angular Gyrus	brain
49	chr6:1949800-1950200	Enhancers	Brain Cingulate Gyrus	brain
50	chr6:1949800-1950200	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links