Variant report

Variant	rs1939488
Chromosome Location	chr11:57062509-57062510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57053497..57056158-chr11:57061828..57064102,2	K562	blood:
2	chr11:57059679..57063275-chr11:57091400..57095134,4	MCF-7	breast:
3	chr11:57059068..57062878-chr11:57064900..57069732,5	K562	blood:
4	chr11:57060644..57063333-chr11:57076469..57078304,2	K562	blood:
5	chr11:57062045..57064988-chr11:57091801..57094620,2	K562	blood:

Variant related genes	Relation type
ENSG00000149115	Chromatin interaction
ENSG00000254662	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1124846	1.00[CEU][hapmap]
rs12786396	0.94[EUR][1000 genomes]
rs12787728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788466	1.00[CEU][hapmap]
rs12797375	0.95[EUR][1000 genomes]
rs12798121	0.87[GIH][hapmap]
rs12799582	1.00[EUR][1000 genomes]
rs12800182	0.87[GIH][hapmap]
rs12801000	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804022	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12806656	0.89[EUR][1000 genomes]
rs12807593	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808193	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808784	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808788	0.94[EUR][1000 genomes]
rs12808989	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17151664	1.00[CEU][hapmap]
rs17151703	1.00[CEU][hapmap]
rs1943488	1.00[CEU][hapmap]
rs2156460	1.00[CEU][hapmap]
rs3017576	1.00[CEU][hapmap]
rs34069781	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34076116	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34085089	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34177110	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34498883	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505638	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34850337	1.00[EUR][1000 genomes]
rs35272228	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35284031	0.87[GIH][hapmap]
rs35366909	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35388927	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35721601	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35950335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35980006	1.00[EUR][1000 genomes]
rs35991636	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36090449	1.00[EUR][1000 genomes]
rs6591419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591420	0.93[AFR][1000 genomes]
rs71484433	1.00[EUR][1000 genomes]
rs71484434	1.00[EUR][1000 genomes]
rs71484435	1.00[EUR][1000 genomes]
rs71484436	1.00[EUR][1000 genomes]
rs71484437	0.95[EUR][1000 genomes]
rs71484440	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484441	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484443	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57052400-57078200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57055200-57063400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:57056800-57064200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:57056800-57065400	Weak transcription	Fetal Heart	heart
5	chr11:57057000-57064800	Weak transcription	Spleen	Spleen
6	chr11:57057000-57065200	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:57057000-57066400	Weak transcription	Colonic Mucosa	Colon
8	chr11:57057000-57066800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:57057200-57065000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:57057200-57065200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:57057200-57066400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:57057200-57066800	Weak transcription	Brain Substantia Nigra	brain
13	chr11:57057400-57063800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:57057400-57064400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:57057400-57065800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:57057400-57066600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:57057800-57064200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:57057800-57064800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:57057800-57065600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:57057800-57066400	Weak transcription	Fetal Kidney	kidney
21	chr11:57058200-57066600	Weak transcription	HUVEC	blood vessel
22	chr11:57058400-57065000	Weak transcription	NHLF	lung
23	chr11:57058800-57062800	Enhancers	Liver	Liver
24	chr11:57059000-57065200	Weak transcription	Fetal Brain Female	brain
25	chr11:57059600-57063400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr11:57059800-57062600	Enhancers	Fetal Muscle Trunk	muscle
27	chr11:57060200-57062800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:57060200-57063600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:57060400-57062600	Enhancers	Placenta	Placenta
30	chr11:57060400-57062800	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:57060400-57062800	Enhancers	Stomach Mucosa	stomach
32	chr11:57060400-57062800	Enhancers	NH-A	brain
33	chr11:57060400-57063000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:57060400-57063200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:57060400-57063400	Enhancers	Esophagus	oesophagus
36	chr11:57060400-57063400	Enhancers	Osteobl	bone
37	chr11:57060400-57063600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr11:57060400-57063600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:57060600-57062600	Enhancers	Gastric	stomach
40	chr11:57060600-57062600	Enhancers	Pancreas	Pancrea
41	chr11:57060600-57062800	Enhancers	Adipose Nuclei	Adipose
42	chr11:57060800-57062800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:57060800-57066600	Weak transcription	K562	blood
44	chr11:57061000-57062600	Enhancers	Brain Germinal Matrix	brain
45	chr11:57061000-57063400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:57061000-57066600	Weak transcription	Fetal Thymus	thymus
47	chr11:57061200-57063000	Enhancers	NHEK	skin
48	chr11:57061200-57065000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:57061200-57066400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr11:57061200-57066800	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links