Variant report

Variant	rs13195362
Chromosome Location	chr6:2356139-2356140
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10458134	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11242751	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11242753	0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11242755	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242756	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189724	1.00[YRI][hapmap]
rs12189730	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12198593	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs12198715	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12207377	0.83[AMR][1000 genomes]
rs12209836	0.86[AMR][1000 genomes]
rs12215421	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12215717	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs12216224	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12523924	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12525444	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12529507	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12529715	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12660715	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664420	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12665003	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12665493	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13194365	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13196348	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13196472	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13202573	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13206299	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13215846	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17134819	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs2129178	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2295009	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs34244401	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34439821	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35063859	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35410074	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3800189	0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes]
rs3817904	1.00[YRI][hapmap]
rs3929752	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58348518	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60015886	0.82[AMR][1000 genomes]
rs73342732	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7452388	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501817	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9647650	0.82[AMR][1000 genomes];0.81[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:28 , 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	chr6:2352000-2362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:2352400-2376400	Weak transcription	HSMMtube	muscle
9	chr6:2352800-2356400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:2352800-2360200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:2353800-2376400	Weak transcription	Pancreas	Pancrea
12	chr6:2354200-2356200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:2354200-2356200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:2354200-2360000	Weak transcription	Fetal Intestine Small	intestine
15	chr6:2354200-2360200	Weak transcription	Fetal Stomach	stomach
16	chr6:2354200-2360400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:2354200-2360800	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:2354200-2362200	Weak transcription	Ovary	ovary
19	chr6:2354200-2363200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:2354200-2363200	Weak transcription	Adipose Nuclei	Adipose
21	chr6:2354200-2366800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:2354200-2367200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:2354200-2371600	Weak transcription	Right Ventricle	heart
24	chr6:2354200-2376400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:2354400-2361000	Weak transcription	Fetal Intestine Large	intestine
26	chr6:2354600-2361800	Weak transcription	Liver	Liver
27	chr6:2355800-2356200	Enhancers	Aorta	Aorta
28	chr6:2356000-2363400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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