Variant report

Variant	rs2479010
Chromosome Location	chr6:2354372-2354373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1894148..1894655-chr6:2354034..2354766,2	K562	blood:
2	chr6:2119577..2122402-chr6:2352666..2355381,2	MCF-7	breast:
3	chr6:2209417..2210065-chr6:2353870..2354459,2	MCF-7	breast:
4	chr6:1604656..1605296-chr6:2353868..2354569,4	MCF-7	breast:
5	chr6:2353810..2354693-chr6:2448790..2449627,3	MCF-7	breast:
6	chr6:1596149..1597077-chr6:2353625..2354389,3	K562	blood:
7	chr6:2208755..2210162-chr6:2353819..2354792,15	MCF-7	breast:
8	chr6:1596534..1597143-chr6:2353875..2354387,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1196389	0.80[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes]
rs1196390	0.90[AMR][1000 genomes]
rs1196393	0.90[AMR][1000 genomes]
rs1196396	0.86[AMR][1000 genomes]
rs1475411	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1486274	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1684153	0.90[AMR][1000 genomes]
rs1887418	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1887420	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2148824	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs234920	0.87[JPT][hapmap]
rs2450301	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2450303	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2450306	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2450311	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2478999	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2479000	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2479003	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2479005	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479009	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479012	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479015	0.92[JPT][hapmap]
rs2505656	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505665	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2505668	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2505669	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2505672	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505674	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs335963	0.81[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes]
rs4959171	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4959648	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62392643	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6596876	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6939099	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7765735	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7766115	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9328086	0.92[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes]
rs9392379	0.86[AMR][1000 genomes]
rs9392382	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9405552	0.83[AMR][1000 genomes]
rs9501828	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[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	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
2	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
3	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
4	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
5	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
6	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
7	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:35 , 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	chr6:2344400-2377400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:2345400-2365800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:2347000-2362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:2349400-2362000	Weak transcription	Spleen	Spleen
6	chr6:2350000-2356600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:2351800-2354400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:2352000-2362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:2352400-2355800	Enhancers	Osteobl	bone
10	chr6:2352400-2376400	Weak transcription	HSMMtube	muscle
11	chr6:2352800-2356400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:2352800-2360200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:2353800-2354600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:2353800-2354600	Active TSS	Aorta	Aorta
15	chr6:2353800-2354600	Enhancers	Liver	Liver
16	chr6:2353800-2354600	Enhancers	HepG2	liver
17	chr6:2353800-2354600	Enhancers	NH-A	brain
18	chr6:2353800-2354800	Enhancers	Hela-S3	cervix
19	chr6:2353800-2376400	Weak transcription	Pancreas	Pancrea
20	chr6:2354000-2354600	Enhancers	Fetal Heart	heart
21	chr6:2354200-2354400	Active TSS	Fetal Lung	lung
22	chr6:2354200-2354600	Enhancers	HUVEC	blood vessel
23	chr6:2354200-2356200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:2354200-2356200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:2354200-2360000	Weak transcription	Fetal Intestine Small	intestine
26	chr6:2354200-2360200	Weak transcription	Fetal Stomach	stomach
27	chr6:2354200-2360400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:2354200-2360800	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:2354200-2362200	Weak transcription	Ovary	ovary
30	chr6:2354200-2363200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:2354200-2363200	Weak transcription	Adipose Nuclei	Adipose
32	chr6:2354200-2366800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:2354200-2367200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:2354200-2371600	Weak transcription	Right Ventricle	heart
35	chr6:2354200-2376400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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