Variant report

Variant	rs6883488
Chromosome Location	chr5:80742290-80742291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10035291	0.81[ASN][1000 genomes]
rs10036712	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10041030	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10042201	0.81[CHB][hapmap]
rs10042303	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10043164	0.80[ASN][1000 genomes]
rs10056711	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10068144	0.87[ASN][1000 genomes]
rs10075648	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10474031	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942266	0.93[ASN][1000 genomes]
rs10942269	0.82[CHD][hapmap]
rs11739075	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740689	0.82[CHD][hapmap]
rs11740719	0.91[CHB][hapmap]
rs11949697	0.91[CHB][hapmap]
rs12153000	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs12697705	0.82[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs13159500	0.88[ASN][1000 genomes]
rs13171682	0.96[ASN][1000 genomes]
rs1541830	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162973	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2396170	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34150522	0.82[ASN][1000 genomes]
rs34699788	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35224297	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764986	0.84[EUR][1000 genomes]
rs3792923	0.91[CEU][hapmap]
rs3805726	0.91[CHB][hapmap]
rs4274955	0.82[CHD][hapmap]
rs4392600	0.82[CHD][hapmap]
rs4513668	0.82[CHD][hapmap]
rs4529168	0.85[CHD][hapmap]
rs6452407	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452409	0.91[CEU][hapmap]
rs6452410	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452411	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6452412	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452414	0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6452415	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452416	1.00[JPT][hapmap]
rs6866156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6866741	0.83[ASN][1000 genomes]
rs6868422	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6868748	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6872775	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6872793	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874029	0.82[CHD][hapmap]
rs6874237	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6874274	0.82[CHD][hapmap]
rs6877102	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6878037	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6880200	0.84[JPT][hapmap]
rs6887937	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6897189	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7702047	0.82[CHD][hapmap]
rs7711020	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7719373	0.84[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7725126	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7725131	0.84[EUR][1000 genomes]
rs7733938	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs7737895	0.83[GIH][hapmap]
rs9293275	0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964102	0.91[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6883488	TMEM167A	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:80704400-80747600	Weak transcription	Placenta	Placenta
3	chr5:80707400-80748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:80709200-80755200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:80713600-80769200	Weak transcription	Esophagus	oesophagus
6	chr5:80716200-80767800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:80716800-80768400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:80717000-80743800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:80717200-80769200	Weak transcription	Right Ventricle	heart
10	chr5:80718000-80768800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:80718400-80752600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:80718400-80754800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:80718400-80755000	Weak transcription	GM12878-XiMat	blood
14	chr5:80719000-80769200	Weak transcription	HSMMtube	muscle
15	chr5:80722000-80754800	Weak transcription	HSMM	muscle
16	chr5:80722400-80746600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:80722400-80754800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:80722400-80755200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:80722400-80768800	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:80722400-80768800	Weak transcription	Fetal Brain Female	brain
21	chr5:80722600-80748600	Weak transcription	Ovary	ovary
22	chr5:80722600-80767600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:80722600-80768000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:80722600-80768200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:80722600-80769000	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:80722600-80769000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:80722600-80769000	Weak transcription	Fetal Brain Male	brain
28	chr5:80722600-80769000	Weak transcription	Psoas Muscle	Psoas
29	chr5:80722600-80769200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:80722800-80744200	Weak transcription	Adipose Nuclei	Adipose
31	chr5:80722800-80747800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:80722800-80748400	Weak transcription	Fetal Lung	lung
33	chr5:80722800-80755200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:80724000-80748400	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:80725200-80748000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:80725400-80755200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:80729600-80769200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:80729800-80769200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:80730600-80767800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:80731400-80749000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:80731400-80768800	Weak transcription	Fetal Kidney	kidney
42	chr5:80731800-80746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:80731800-80746400	Weak transcription	Primary B cells from cord blood	blood
44	chr5:80731800-80769200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:80732000-80748200	Weak transcription	Thymus	Thymus
46	chr5:80733600-80756000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:80734000-80746800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:80734400-80748400	Weak transcription	K562	blood
49	chr5:80735400-80778600	Weak transcription	Aorta	Aorta
50	chr5:80735600-80745600	Weak transcription	Fetal Stomach	stomach

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