Variant report

Variant	rs12777477
Chromosome Location	chr10:5912143-5912144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5910241..5913072-chr10:5913979..5917301,3	MCF-7	breast:
2	chr10:5853596..5857884-chr10:5911550..5919142,12	MCF-7	breast:
3	chr10:5854510..5857923-chr10:5911220..5914905,6	MCF-7	breast:
4	chr10:5912116..5916503-chr10:5917203..5921455,4	K562	blood:
5	chr10:5911390..5913912-chr10:5936445..5939123,2	MCF-7	breast:
6	chr10:5910337..5913057-chr10:5913896..5915551,2	K562	blood:
7	chr10:5912116..5915465-chr10:5917203..5919997,3	K562	blood:
8	chr10:5912111..5919800-chr10:5923492..5927477,10	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GDI2-3	chr10:5911773-5912346	NONHSAT011188

No data

Variant related genes	Relation type
ENSG00000272764	Chromatin interaction
ENSG00000057608	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10508298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10508299	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11255527	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11255548	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11255581	0.83[EUR][1000 genomes]
rs11255662	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11255780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11255974	1.00[CHB][hapmap]
rs11524382	0.83[EUR][1000 genomes]
rs11819695	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12359234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12360409	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12769593	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12774228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12774886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12779398	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12780246	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12785055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17319759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2104285	0.82[EUR][1000 genomes]
rs2203196	0.82[EUR][1000 genomes]
rs2203197	0.81[EUR][1000 genomes]
rs2380201	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2387092	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3209286	1.00[JPT][hapmap]
rs4428973	0.80[EUR][1000 genomes]
rs6602330	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6602819	1.00[JPT][hapmap]
rs7067928	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7073128	0.83[EUR][1000 genomes]
rs7082434	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7090411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7893735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7919913	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs867053	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs907686	0.81[EUR][1000 genomes]
rs907688	0.81[EUR][1000 genomes]
rs907689	0.81[EUR][1000 genomes]
rs907690	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9424204	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv466722	chr10:5893268-5916201	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv549904	chr10:5893268-5916201	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5894600-5916800	Weak transcription	Spleen	Spleen
2	chr10:5896200-5912200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr10:5896400-5918200	Weak transcription	Fetal Lung	lung
4	chr10:5900000-5916600	Weak transcription	Pancreas	Pancrea
5	chr10:5900400-5916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:5900600-5916200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:5901000-5916600	Weak transcription	Gastric	stomach
8	chr10:5901200-5918200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:5901400-5915200	Weak transcription	Brain Hippocampus Middle	brain
10	chr10:5901600-5912600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:5901600-5915600	Weak transcription	Brain Anterior Caudate	brain
12	chr10:5902200-5912600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:5902400-5918200	Weak transcription	Primary T cells from cord blood	blood
14	chr10:5902800-5916200	Weak transcription	Fetal Intestine Large	intestine
15	chr10:5902800-5916600	Weak transcription	Brain Substantia Nigra	brain
16	chr10:5902800-5918000	Weak transcription	Lung	lung
17	chr10:5903000-5912400	Weak transcription	Fetal Heart	heart
18	chr10:5903000-5915400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:5903400-5918200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr10:5903400-5925000	Weak transcription	Fetal Kidney	kidney
21	chr10:5903600-5916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:5903800-5913600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:5903800-5916000	Weak transcription	NHEK	skin
24	chr10:5903800-5916400	Weak transcription	A549	lung
25	chr10:5903800-5918200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:5904400-5916200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:5904400-5916200	Weak transcription	Aorta	Aorta
28	chr10:5904600-5915600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:5904600-5916200	Weak transcription	NHDF-Ad	bronchial
30	chr10:5905000-5913400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:5905000-5916200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:5905000-5916200	Weak transcription	Brain Angular Gyrus	brain
33	chr10:5905200-5918200	Weak transcription	HepG2	liver
34	chr10:5908800-5918400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:5909400-5915600	Weak transcription	K562	blood
36	chr10:5909400-5916400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:5909400-5918200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr10:5909600-5924800	Weak transcription	Stomach Mucosa	stomach
39	chr10:5909800-5912800	Weak transcription	Psoas Muscle	Psoas
40	chr10:5909800-5914800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr10:5909800-5918200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:5910200-5914000	Strong transcription	Fetal Stomach	stomach
43	chr10:5910600-5916600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr10:5911000-5912600	Weak transcription	Fetal Muscle Leg	muscle
45	chr10:5911000-5912800	Weak transcription	Fetal Intestine Small	intestine
46	chr10:5911000-5916200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:5911200-5912600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:5911200-5916200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr10:5911200-5918200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:5911400-5912800	Weak transcription	Left Ventricle	heart

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