Variant report

Variant	rs11940990
Chromosome Location	chr4:125859303-125859304
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:125857080..125860001-chr4:125867292..125869846,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10006172	0.91[ASN][1000 genomes]
rs11931077	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11931654	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11932360	0.91[ASN][1000 genomes]
rs11936463	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11936464	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13102212	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13108189	0.91[ASN][1000 genomes]
rs13108522	0.91[ASN][1000 genomes]
rs13129944	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149362	0.83[EUR][1000 genomes]
rs13151922	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1498044	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17008772	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17008804	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17008868	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1817524	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1848055	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1911130	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2390767	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28559639	0.91[ASN][1000 genomes]
rs35283842	0.91[ASN][1000 genomes]
rs35370493	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35420046	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35500952	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56107106	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59008121	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67619349	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6834370	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6841865	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846803	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6847185	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6847509	0.82[ASN][1000 genomes]
rs6851962	0.91[ASN][1000 genomes]
rs6852823	0.91[ASN][1000 genomes]
rs6853549	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610104	0.83[EUR][1000 genomes]
rs71610105	0.83[EUR][1000 genomes]
rs9637631	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9993806	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	nsv1011752	chr4:125708756-125932456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1001338	chr4:125708756-126103293	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv830050	chr4:125717858-125888563	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125844800-125860600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:125856200-125860600	Enhancers	Fetal Muscle Leg	muscle
3	chr4:125856200-125866800	Enhancers	Hela-S3	cervix
4	chr4:125856400-125860400	Weak transcription	NHEK	skin
5	chr4:125856600-125859800	Enhancers	Fetal Heart	heart
6	chr4:125856600-125860600	Weak transcription	Right Ventricle	heart
7	chr4:125857600-125859600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr4:125857600-125862600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:125857800-125859600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr4:125857800-125861400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:125858000-125859400	Weak transcription	Osteobl	bone
12	chr4:125858000-125860000	Weak transcription	HUVEC	blood vessel
13	chr4:125858000-125860200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:125858000-125860200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:125858000-125860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:125858000-125860400	Weak transcription	Lung	lung
17	chr4:125858000-125860400	Weak transcription	Right Atrium	heart
18	chr4:125858000-125860800	Weak transcription	NH-A	brain
19	chr4:125858000-125861200	Weak transcription	Adipose Nuclei	Adipose
20	chr4:125858000-125861400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:125858000-125865000	Weak transcription	Ovary	ovary
22	chr4:125858000-125868000	Weak transcription	Pancreas	Pancrea
23	chr4:125858200-125859400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:125858200-125859400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:125858200-125859400	Weak transcription	HSMM	muscle
26	chr4:125858200-125860200	Weak transcription	NHLF	lung
27	chr4:125858200-125861400	Weak transcription	Stomach Mucosa	stomach
28	chr4:125858200-125867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:125858400-125859400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:125858600-125859400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:125858600-125859600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:125858600-125859600	Enhancers	Left Ventricle	heart
33	chr4:125858600-125859800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr4:125858600-125861000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:125858800-125859400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr4:125858800-125859600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr4:125858800-125859600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr4:125859000-125859400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:125859000-125859400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:125859000-125859400	Enhancers	Psoas Muscle	Psoas
41	chr4:125859000-125859600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:125859000-125861200	Weak transcription	Fetal Stomach	stomach
43	chr4:125859000-125861600	Weak transcription	Fetal Kidney	kidney
44	chr4:125859200-125859400	Enhancers	Esophagus	oesophagus
45	chr4:125859200-125859400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr4:125859200-125859600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:125859200-125859600	Enhancers	HSMMtube	muscle
48	chr4:125859200-125859800	Enhancers	Gastric	stomach
49	chr4:125859200-125861200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:125859200-125862800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links