Variant report

Variant	rs10499259
Chromosome Location	chr6:149211090-149211091
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	chr15:23001522..23002177-chr6:149210634..149211252,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11756841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11757486	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758175	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11758187	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11758230	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11759833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1340498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1340499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1351698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1351699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1545840	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545841	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17079451	0.83[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap]
rs17079511	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1817508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34443186	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35526080	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35748463	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35946167	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56904209	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62426104	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62426110	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv464074	chr6:149211090-149242095	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv604844	chr6:149211090-149242095	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149193200-149218800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:149199400-149215600	Weak transcription	Spleen	Spleen
3	chr6:149203400-149213400	Weak transcription	Dnd41	blood
4	chr6:149205400-149211200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:149206000-149212600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:149206200-149212600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:149206400-149211800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:149206400-149212400	Enhancers	Fetal Muscle Leg	muscle
9	chr6:149207400-149211400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:149207400-149214800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:149207800-149219400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:149207800-149221400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:149207800-149237400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:149208000-149217200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:149208000-149229800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:149208600-149213200	Weak transcription	NHLF	lung
17	chr6:149208800-149211800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:149209000-149212600	Enhancers	Ovary	ovary
19	chr6:149209000-149213200	Weak transcription	NHEK	skin
20	chr6:149209000-149247600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:149209600-149213200	Enhancers	Fetal Heart	heart
22	chr6:149209600-149214800	Weak transcription	Fetal Stomach	stomach
23	chr6:149209800-149211200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:149209800-149211400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:149209800-149230800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:149210000-149211600	Enhancers	Stomach Smooth Muscle	stomach
27	chr6:149210000-149212400	Enhancers	HSMMtube	muscle
28	chr6:149210000-149218000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:149210000-149220800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:149210200-149211200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:149210200-149211400	Weak transcription	Fetal Brain Female	brain
32	chr6:149210200-149211600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:149210200-149211600	Enhancers	Adipose Nuclei	Adipose
34	chr6:149210200-149212400	Enhancers	Fetal Muscle Trunk	muscle
35	chr6:149210200-149212600	Enhancers	Aorta	Aorta
36	chr6:149210200-149212600	Enhancers	Fetal Lung	lung
37	chr6:149210200-149212600	Enhancers	Right Atrium	heart
38	chr6:149210200-149212600	Enhancers	Osteobl	bone
39	chr6:149210200-149212800	Enhancers	Stomach Mucosa	stomach
40	chr6:149210200-149230200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:149210200-149240200	Weak transcription	Primary B cells from cord blood	blood
42	chr6:149210400-149211400	Weak transcription	Fetal Brain Male	brain
43	chr6:149210400-149214800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:149210400-149226200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:149210400-149235000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:149210600-149211400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr6:149210800-149211200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:149210800-149211600	Enhancers	Left Ventricle	heart
49	chr6:149210800-149211600	Enhancers	HSMM	muscle
50	chr6:149210800-149226000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links