Variant report

Variant	rs7610686
Chromosome Location	chr3:78705219-78705220
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:80)

rs_ID	r²[population]
rs10049014	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10049102	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10428105	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914618	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11915494	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915745	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917512	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11918759	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11920344	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11925970	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927666	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11928868	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12106862	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1395784	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1457659	0.90[CEU][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs17016453	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17016466	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17303276	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17375110	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17375496	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17375739	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs1865860	0.89[CEU][hapmap]
rs1865861	0.89[CEU][hapmap]
rs1865863	0.90[CEU][hapmap]
rs2031051	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118068	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271151	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732662	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732663	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3773220	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs3773224	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773225	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773226	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773227	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3773231	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3773234	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap]
rs3773240	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3821601	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821602	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3821603	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs4263256	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56372508	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58561177	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60568341	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60749216	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61053911	0.83[EUR][1000 genomes]
rs67137735	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67347336	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67362360	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67498832	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769933	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6787349	0.90[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs6788434	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6788511	0.90[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806079	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73109717	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73850750	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610500	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7613490	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7616495	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622194	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624482	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7653782	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs767182	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309810	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9309811	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9309814	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9808950	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9818170	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819398	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9823359	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829907	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9831098	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9840004	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9866912	0.89[CEU][hapmap]
rs9880072	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880316	0.90[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882811	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883582	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs997274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78654200-78708800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:78654200-78746600	Weak transcription	NHDF-Ad	bronchial
3	chr3:78654800-78706800	Weak transcription	NHLF	lung
4	chr3:78654800-78711000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:78656000-78718600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:78656200-78711000	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:78664000-78710200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:78667200-78706600	Weak transcription	Gastric	stomach
9	chr3:78667200-78751200	Weak transcription	Esophagus	oesophagus
10	chr3:78676800-78730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:78679200-78720800	Weak transcription	Aorta	Aorta
12	chr3:78679200-78733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:78679400-78710600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:78679400-78730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:78679400-78736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:78680400-78717800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:78680400-78723600	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:78682800-78715000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:78682800-78720200	Weak transcription	Adipose Nuclei	Adipose
20	chr3:78683000-78711000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:78689000-78705800	Weak transcription	Primary T cells from cord blood	blood
22	chr3:78693400-78730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:78694200-78730600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:78694400-78713600	Weak transcription	Fetal Brain Male	brain
25	chr3:78694400-78718400	Weak transcription	Fetal Heart	heart
26	chr3:78694400-78733200	Weak transcription	Fetal Kidney	kidney
27	chr3:78695000-78711200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:78695400-78709800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:78695400-78711000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:78696800-78719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:78697200-78715000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:78697400-78715000	Weak transcription	NHEK	skin
33	chr3:78697800-78715400	Weak transcription	NH-A	brain
34	chr3:78698400-78717000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:78699200-78706400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:78702400-78706400	Strong transcription	Fetal Lung	lung
37	chr3:78702400-78707000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:78702800-78705800	Weak transcription	Brain Germinal Matrix	brain
39	chr3:78702800-78706400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:78702800-78730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:78703000-78705800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:78703000-78717200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:78703200-78739200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:78704200-78706600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr3:78704400-78706200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:78704400-78706400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:78704400-78707000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:78704400-78707000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:78704600-78705400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:78704600-78706200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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