Variant report

Variant	rs9827888
Chromosome Location	chr3:69984363-69984364
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11128144	0.87[EUR][1000 genomes]
rs11128145	0.87[EUR][1000 genomes]
rs11128146	0.87[EUR][1000 genomes]
rs11128147	0.87[EUR][1000 genomes]
rs11128148	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11128149	0.87[EUR][1000 genomes]
rs11128150	0.87[EUR][1000 genomes]
rs11128151	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11128154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12106831	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12106842	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12106907	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12106913	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12106915	0.87[EUR][1000 genomes]
rs12107208	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12107258	0.87[EUR][1000 genomes]
rs12107267	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12107268	0.87[EUR][1000 genomes]
rs12107403	0.87[EUR][1000 genomes]
rs12107405	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12107409	0.87[EUR][1000 genomes]
rs12107473	0.87[EUR][1000 genomes]
rs12107744	1.00[CHB][hapmap]
rs12108172	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12108174	0.87[EUR][1000 genomes]
rs1430600	0.87[EUR][1000 genomes]
rs1532199	1.00[CHB][hapmap]
rs17006441	1.00[CHB][hapmap]
rs17006565	1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs17006574	0.89[EUR][1000 genomes]
rs17006578	1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs17006580	0.87[EUR][1000 genomes]
rs17006582	0.87[EUR][1000 genomes]
rs17006587	0.87[EUR][1000 genomes]
rs17006593	0.87[EUR][1000 genomes]
rs17006595	0.87[EUR][1000 genomes]
rs17006597	0.87[EUR][1000 genomes]
rs17006601	0.87[EUR][1000 genomes]
rs17006609	0.87[EUR][1000 genomes]
rs28480308	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6549252	1.00[CHB][hapmap]
rs724794	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs9310177	1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837137	0.89[EUR][1000 genomes]
rs9840417	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs9843596	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs9843611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9847658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866423	1.00[CHB][hapmap];0.84[YRI][hapmap]
rs9882545	1.00[YRI][hapmap]
rs9882576	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917634	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917686	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9917798	0.87[EUR][1000 genomes]
rs9941978	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69964400-70008400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:69971600-69985200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:69974800-69989600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:69975000-69987000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:69975000-69987200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:69975200-69989600	Weak transcription	Adipose Nuclei	Adipose
7	chr3:69975200-69997000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:69975200-70008400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:69975800-69987000	Weak transcription	Pancreas	Pancrea
10	chr3:69975800-70008400	Weak transcription	Aorta	Aorta
11	chr3:69975800-70013800	Weak transcription	Psoas Muscle	Psoas
12	chr3:69978400-69987000	Weak transcription	Lung	lung
13	chr3:69978600-70014000	Weak transcription	Esophagus	oesophagus
14	chr3:69979800-69987000	Weak transcription	Gastric	stomach
15	chr3:69979800-69987000	Weak transcription	Ovary	ovary
16	chr3:69979800-70008400	Weak transcription	Right Ventricle	heart
17	chr3:69980000-69987000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:69980000-69989400	Weak transcription	Left Ventricle	heart
19	chr3:69980400-69987000	Weak transcription	Brain Anterior Caudate	brain
20	chr3:69980600-69988800	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:69981800-69985200	Weak transcription	Fetal Heart	heart
22	chr3:69981800-69990600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:69981800-70008200	Weak transcription	Stomach Mucosa	stomach
24	chr3:69981800-70016800	Weak transcription	K562	blood
25	chr3:69982000-69987200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:69983000-69986400	Enhancers	Brain Hippocampus Middle	brain
27	chr3:69983200-69984400	Enhancers	Brain Angular Gyrus	brain
28	chr3:69983200-69984800	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:69983200-69985400	Enhancers	Brain Substantia Nigra	brain
30	chr3:69983200-69985600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:69983400-70008400	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:69983600-69984600	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr3:69983600-69984800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:69984000-70008600	Weak transcription	Fetal Kidney	kidney

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