Variant report

Variant	rs9851771
Chromosome Location	chr3:48531740-48531741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1003649	1.00[GIH][hapmap]
rs10049154	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10470687	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs13060933	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13063312	0.83[GIH][hapmap]
rs13064619	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13070798	0.83[GIH][hapmap]
rs13091944	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100178	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319635	0.81[ASN][1000 genomes]
rs13319651	0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs13324142	0.83[GIH][hapmap]
rs1459247	1.00[JPT][hapmap]
rs17080289	0.83[GIH][hapmap]
rs2006871	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs2276850	0.83[GIH][hapmap]
rs2276852	0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap]
rs2310996	0.83[GIH][hapmap]
rs2854394	0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs28563843	0.86[ASN][1000 genomes]
rs28881595	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35562294	0.82[ASN][1000 genomes]
rs3755819	0.82[ASN][1000 genomes]
rs3821876	0.83[GIH][hapmap]
rs3969942	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075082	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442126	1.00[CHB][hapmap]
rs6442127	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765317	0.94[ASN][1000 genomes]
rs6781283	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs6785845	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786424	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792156	0.83[GIH][hapmap]
rs6792525	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs6806059	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs6809981	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740787	0.83[GIH][hapmap]
rs7428949	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7434077	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7434107	1.00[ASN][1000 genomes]
rs7623614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631574	0.83[GIH][hapmap]
rs7640031	1.00[ASN][1000 genomes]
rs7644771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs9810991	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822677	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830581	0.83[GIH][hapmap]
rs9835827	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836462	0.83[GIH][hapmap]
rs9837687	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap]
rs9843316	0.83[GIH][hapmap]
rs9848824	0.86[ASN][1000 genomes]
rs9849280	0.86[ASN][1000 genomes]
rs9850102	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9851743	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864729	0.86[ASN][1000 genomes]
rs9869698	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs9871608	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875911	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs9878950	0.80[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs9881877	0.80[CHD][hapmap];0.83[GIH][hapmap];0.82[ASN][1000 genomes]
rs9882962	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48514600-48535600	Weak transcription	Ovary	ovary
2	chr3:48514800-48541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:48515000-48532800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:48515000-48533000	Weak transcription	NH-A	brain
5	chr3:48515000-48535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:48515000-48535600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:48515000-48537400	Weak transcription	NHLF	lung
8	chr3:48515000-48539600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:48515000-48539800	Weak transcription	Osteobl	bone
10	chr3:48515000-48540200	Weak transcription	NHDF-Ad	bronchial
11	chr3:48515000-48540400	Weak transcription	HSMM	muscle
12	chr3:48515000-48541000	Weak transcription	Aorta	Aorta
13	chr3:48515200-48535000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:48515200-48535000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:48515200-48535600	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:48515200-48535600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:48515200-48537400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:48515200-48538600	Weak transcription	Small Intestine	intestine
19	chr3:48515200-48539800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:48515200-48540000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:48515200-48540200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:48515200-48540200	Weak transcription	HUVEC	blood vessel
23	chr3:48515200-48540400	Weak transcription	Fetal Brain Female	brain
24	chr3:48515200-48540600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:48515200-48540600	Weak transcription	Fetal Lung	lung
26	chr3:48515400-48535600	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:48515400-48538200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:48516600-48535000	Weak transcription	Fetal Intestine Large	intestine
29	chr3:48516600-48535600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:48516800-48534200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:48516800-48535600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:48517000-48535600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:48517200-48534400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:48517200-48537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:48517200-48540400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:48517200-48540400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:48518200-48535600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:48518400-48532600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:48519200-48534200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:48519400-48532600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:48519600-48538600	Weak transcription	Right Atrium	heart
42	chr3:48519600-48540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:48519800-48532800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:48519800-48532800	Weak transcription	Adipose Nuclei	Adipose
45	chr3:48519800-48539600	Weak transcription	Right Ventricle	heart
46	chr3:48520000-48532600	Weak transcription	Placenta	Placenta
47	chr3:48520000-48535200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:48520600-48534400	Weak transcription	Lung	lung
49	chr3:48520600-48538200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:48520800-48532800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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