Variant report

Variant	rs2479000
Chromosome Location	chr6:2306501-2306502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1196389	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1196390	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196393	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196396	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1475411	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1486274	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1684153	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1887418	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1887420	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2148824	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2450301	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450303	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2450306	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2450311	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2478999	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2479003	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2479005	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2479009	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2479010	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2479012	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2505656	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505665	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505668	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505669	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505672	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2505674	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs335963	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4959171	0.91[ASN][1000 genomes]
rs4959648	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62392643	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6596876	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6939099	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7765735	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7766115	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9328086	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9392379	0.88[AMR][1000 genomes]
rs9392382	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9405552	0.91[AMR][1000 genomes]
rs9501828	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
9	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
12	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
15	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
16	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
17	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2275400-2319400	Weak transcription	Gastric	stomach
2	chr6:2298400-2320400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:2299000-2319600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:2299200-2324200	Weak transcription	Aorta	Aorta
5	chr6:2299800-2316800	Weak transcription	Left Ventricle	heart
6	chr6:2306000-2306600	Active TSS	Duodenum Mucosa	Duodenum
7	chr6:2306000-2307400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:2306000-2316800	Weak transcription	Fetal Stomach	stomach
9	chr6:2306200-2306600	ZNF genes & repeats	Ovary	ovary
10	chr6:2306200-2306600	Enhancers	HepG2	liver
11	chr6:2306400-2306600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:2306400-2314600	Weak transcription	Primary hematopoietic stem cells	blood

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