Variant report

Variant	rs2178339
Chromosome Location	chr10:49540590-49540591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49517538..49519332-chr10:49540338..49542175,2	MCF-7	breast:
2	chr10:49538148..49542508-chr10:49545021..49547777,3	K562	blood:
3	chr10:49423310..49424126-chr10:49540299..49540827,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10745265	0.86[ASN][1000 genomes]
rs10776592	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776593	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776594	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857563	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857564	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857565	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1112268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597435	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11598320	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12358297	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17780725	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1881735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1881737	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881738	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881740	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881741	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1919706	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1919707	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919709	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1997365	0.86[ASN][1000 genomes]
rs2141516	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377140	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2377141	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2377349	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590382	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2590383	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590384	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590385	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2590386	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590391	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2698758	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2698762	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2698768	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2889595	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4012930	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4838405	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4838588	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56078229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6537559	0.86[ASN][1000 genomes]
rs7068398	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7084326	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7898026	0.81[ASN][1000 genomes]
rs9919504	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv6587	chr10:49526329-49571804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv947976	chr10:49537663-49541857	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 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	chr10:49515600-49541400	Weak transcription	Lung	lung
2	chr10:49516400-49541400	Weak transcription	Right Atrium	heart
3	chr10:49516400-49547200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:49516400-49559600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:49517800-49544600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:49518200-49542200	Weak transcription	HSMM	muscle
7	chr10:49518800-49540600	Weak transcription	NHEK	skin
8	chr10:49518800-49542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:49518800-49544000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:49520200-49549800	Weak transcription	HUVEC	blood vessel
11	chr10:49522800-49550800	Weak transcription	Small Intestine	intestine
12	chr10:49525000-49541600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:49525800-49551800	Weak transcription	Adipose Nuclei	Adipose
14	chr10:49526200-49552000	Weak transcription	NH-A	brain
15	chr10:49529000-49550800	Weak transcription	K562	blood
16	chr10:49530200-49540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:49530800-49554600	Weak transcription	Fetal Brain Male	brain
18	chr10:49535000-49541800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:49535200-49541400	Weak transcription	Esophagus	oesophagus
20	chr10:49535400-49548200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:49536800-49541800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr10:49536800-49545200	Weak transcription	Brain Angular Gyrus	brain
23	chr10:49537400-49541800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr10:49538400-49541000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr10:49538400-49541000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr10:49538400-49541200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr10:49538400-49541200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:49538400-49541600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:49538400-49543200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr10:49538400-49543200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:49538600-49540600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:49538600-49541000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr10:49538600-49541000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr10:49538600-49541000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr10:49538600-49541000	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr10:49538600-49541200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:49538600-49541200	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr10:49538600-49541200	ZNF genes & repeats	Fetal Lung	lung
39	chr10:49538600-49541800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr10:49538600-49542200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:49538600-49542800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:49538600-49542800	ZNF genes & repeats	Brain Germinal Matrix	brain
43	chr10:49538600-49543000	ZNF genes & repeats	Fetal Stomach	stomach
44	chr10:49538600-49545400	Weak transcription	Hela-S3	cervix
45	chr10:49538600-49551400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:49538800-49540800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr10:49538800-49541800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr10:49538800-49542800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:49538800-49543000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:49538800-49544600	Weak transcription	Spleen	Spleen

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