Variant report

Variant	rs2479009
Chromosome Location	chr6:2350020-2350021
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1196389	0.86[AMR][1000 genomes]
rs1196390	0.88[AMR][1000 genomes]
rs1196393	0.88[AMR][1000 genomes]
rs1196396	0.84[AMR][1000 genomes]
rs1475411	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1486274	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1684153	0.88[AMR][1000 genomes]
rs1887418	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887420	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2148824	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450301	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2450303	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2450306	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450311	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2478999	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2479000	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2479003	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2479005	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479012	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505656	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505665	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2505668	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2505669	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2505672	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2505674	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs335963	0.86[AMR][1000 genomes]
rs4959171	1.00[ASN][1000 genomes]
rs4959648	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392643	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6596876	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6939099	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7765735	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766115	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328086	0.86[AMR][1000 genomes]
rs9392379	0.84[AMR][1000 genomes]
rs9392382	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9405552	0.81[AMR][1000 genomes]
rs9501828	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	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	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
4	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
5	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
6	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
7	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
8	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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2339200-2370000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:2344400-2353600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:2344400-2377400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:2345400-2365800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:2345600-2353800	Weak transcription	Fetal Stomach	stomach
6	chr6:2346600-2352000	Weak transcription	Aorta	Aorta
7	chr6:2346600-2353800	Weak transcription	HepG2	liver
8	chr6:2347000-2351000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:2347000-2362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:2347400-2352000	Weak transcription	HSMMtube	muscle
11	chr6:2349400-2362000	Weak transcription	Spleen	Spleen
12	chr6:2349600-2353800	Weak transcription	Stomach Mucosa	stomach
13	chr6:2350000-2356600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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