Variant report

Variant	rs3797825
Chromosome Location	chr5:108294075-108294076
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10043207	0.81[JPT][hapmap]
rs10061582	0.82[ASN][1000 genomes]
rs10062069	0.82[JPT][hapmap]
rs10515399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11948270	0.81[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11950165	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11951595	0.82[CEU][hapmap]
rs11953198	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs11955924	0.82[CEU][hapmap]
rs11956900	0.81[EUR][1000 genomes]
rs11958129	0.82[CEU][hapmap]
rs11960268	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11960336	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11960400	0.83[CEU][hapmap]
rs12153527	0.83[CEU][hapmap]
rs12153646	0.83[CEU][hapmap]
rs1366081	0.82[JPT][hapmap]
rs1896582	0.82[JPT][hapmap]
rs2416197	0.82[JPT][hapmap]
rs28733366	0.85[ASN][1000 genomes]
rs3797818	0.93[ASN][1000 genomes]
rs3797819	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3797820	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3797821	0.93[ASN][1000 genomes]
rs3797823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797832	0.82[JPT][hapmap]
rs3797833	0.82[JPT][hapmap]
rs3822684	0.82[CEU][hapmap]
rs4404726	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4957793	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55899933	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56121551	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57158292	0.85[AFR][1000 genomes]
rs57814250	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58647764	0.96[ASN][1000 genomes]
rs58729959	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60834821	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66623856	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66851282	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67053762	0.90[ASN][1000 genomes]
rs67586696	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6861439	0.81[ASN][1000 genomes]
rs6865572	0.82[JPT][hapmap]
rs6867147	0.81[EUR][1000 genomes]
rs6872299	0.83[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6884648	0.96[ASN][1000 genomes]
rs6893501	0.87[CEU][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6893984	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72789336	0.81[EUR][1000 genomes]
rs72789338	0.81[EUR][1000 genomes]
rs72789339	0.81[EUR][1000 genomes]
rs72790513	0.81[EUR][1000 genomes]
rs72793921	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73209364	0.98[ASN][1000 genomes]
rs73209368	1.00[ASN][1000 genomes]
rs73209370	0.97[ASN][1000 genomes]
rs73211527	0.97[ASN][1000 genomes]
rs73211528	0.97[ASN][1000 genomes]
rs73211549	0.96[ASN][1000 genomes]
rs73211553	0.96[ASN][1000 genomes]
rs73211559	0.96[ASN][1000 genomes]
rs73211560	0.96[ASN][1000 genomes]
rs73778332	0.98[ASN][1000 genomes]
rs73778336	0.97[ASN][1000 genomes]
rs73778344	0.96[ASN][1000 genomes]
rs73778358	0.96[ASN][1000 genomes]
rs73778371	0.81[EUR][1000 genomes]
rs7719638	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7723942	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7726922	0.94[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs7731116	0.98[ASN][1000 genomes]
rs7731221	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7732335	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7732510	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7734092	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7734110	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7735749	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv525993	chr5:108288345-108299744	Strong transcription Enhancers Weak transcription	miRNA target site	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
3	chr5:108230200-108302400	Weak transcription	HSMM	muscle
4	chr5:108244200-108295000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:108254000-108311200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:108268400-108301400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:108277600-108322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:108278000-108308200	Weak transcription	Fetal Kidney	kidney
9	chr5:108279000-108295000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:108279200-108302600	Weak transcription	Ovary	ovary
11	chr5:108279200-108325600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:108279800-108295200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:108281000-108302400	Weak transcription	Dnd41	blood
14	chr5:108281000-108302600	Weak transcription	HMEC	breast
15	chr5:108281000-108313400	Weak transcription	Adipose Nuclei	Adipose
16	chr5:108281200-108302600	Weak transcription	Brain Angular Gyrus	brain
17	chr5:108281600-108296800	Weak transcription	Fetal Heart	heart
18	chr5:108282200-108324600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:108282400-108327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:108282800-108294800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:108283400-108319000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:108287800-108310000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:108289200-108309200	Weak transcription	Hela-S3	cervix
24	chr5:108289200-108318600	Weak transcription	NHDF-Ad	bronchial
25	chr5:108290000-108313600	Weak transcription	Aorta	Aorta
26	chr5:108290000-108322000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:108290000-108328800	Weak transcription	Esophagus	oesophagus
28	chr5:108292600-108302600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:108293400-108303400	Weak transcription	Fetal Lung	lung
30	chr5:108293400-108325600	Weak transcription	NHEK	skin
31	chr5:108294000-108302600	Weak transcription	Liver	Liver

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