Variant report

Variant	rs17077109
Chromosome Location	chr8:6339343-6339344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1054073	0.89[JPT][hapmap]
rs11137029	1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11137033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1129703	0.82[JPT][hapmap]
rs1129704	0.94[JPT][hapmap]
rs1129706	0.89[JPT][hapmap]
rs12546890	0.82[CEU][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs12550299	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs12674488	1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12675930	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs12676907	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs12676922	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12677501	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679619	1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs12680048	1.00[ASN][1000 genomes]
rs12681009	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12681195	0.81[EUR][1000 genomes]
rs13248420	0.82[CEU][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13267816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs13281793	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13281967	0.81[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13282022	0.82[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13282116	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13282577	0.82[CEU][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1373307	0.94[JPT][hapmap]
rs1550690	0.94[JPT][hapmap]
rs17077056	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17077067	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17077083	0.82[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs17077094	0.82[CEU][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs17613024	0.82[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867385	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs1867386	0.89[JPT][hapmap]
rs1868551	0.89[JPT][hapmap]
rs1868555	0.92[ASN][1000 genomes]
rs2034143	0.90[CHD][hapmap];0.94[JPT][hapmap]
rs2251956	0.83[JPT][hapmap]
rs2254903	0.83[JPT][hapmap]
rs2277136	0.86[ASW][hapmap];0.82[CEU][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs2440392	0.87[ASN][1000 genomes]
rs2440396	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2440397	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2440399	0.89[CEU][hapmap]
rs2440406	0.94[JPT][hapmap]
rs2440412	0.94[JPT][hapmap]
rs2440414	0.89[JPT][hapmap]
rs2440416	0.94[JPT][hapmap]
rs2440422	0.89[JPT][hapmap]
rs2440423	0.83[JPT][hapmap]
rs2440424	0.83[JPT][hapmap]
rs2440427	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs2440428	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2440430	0.84[CHB][hapmap]
rs2440432	0.94[JPT][hapmap]
rs2442483	0.91[ASN][1000 genomes]
rs2442485	0.94[JPT][hapmap]
rs2442490	0.89[CEU][hapmap]
rs2442491	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2442492	0.89[CEU][hapmap]
rs2442493	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2442496	0.89[CEU][hapmap]
rs2442497	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs2442500	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2442502	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs2442510	0.89[JPT][hapmap]
rs2442511	0.94[JPT][hapmap]
rs2442516	0.89[JPT][hapmap]
rs2442517	0.89[JPT][hapmap]
rs2442518	0.83[JPT][hapmap]
rs2442521	0.85[JPT][hapmap]
rs2442522	0.83[JPT][hapmap]
rs2442523	0.94[JPT][hapmap]
rs2442524	0.94[JPT][hapmap]
rs2442536	0.84[JPT][hapmap]
rs2442546	0.84[JPT][hapmap]
rs2515572	0.91[CHD][hapmap];0.94[JPT][hapmap]
rs2515574	0.85[CHB][hapmap]
rs2515585	0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2916740	0.89[JPT][hapmap]
rs2916741	0.89[JPT][hapmap]
rs2916742	0.89[JPT][hapmap]
rs2916743	0.89[JPT][hapmap]
rs2916746	0.89[JPT][hapmap]
rs2916750	0.89[JPT][hapmap]
rs2920659	0.94[JPT][hapmap]
rs2920660	0.89[JPT][hapmap]
rs2920665	0.89[JPT][hapmap]
rs2920671	0.89[JPT][hapmap]
rs2920674	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2920677	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2920678	0.93[ASN][1000 genomes]
rs2920681	0.94[CEU][hapmap];0.94[JPT][hapmap]
rs2920689	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2922811	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2922813	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2922814	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2922815	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2922818	0.89[JPT][hapmap]
rs2922820	0.89[JPT][hapmap]
rs2979648	0.94[JPT][hapmap]
rs2979652	0.89[JPT][hapmap]
rs2979655	0.89[CEU][hapmap]
rs2979664	0.93[ASN][1000 genomes]
rs3020270	0.89[JPT][hapmap]
rs3020289	0.87[ASN][1000 genomes]
rs34009442	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635086	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748476	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35150903	0.82[ASN][1000 genomes]
rs35248379	0.87[ASN][1000 genomes]
rs56073811	0.81[EUR][1000 genomes]
rs57804372	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58679306	0.94[ASN][1000 genomes]
rs59635757	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60915478	0.81[EUR][1000 genomes]
rs6559164	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs6989935	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6994734	0.84[JPT][hapmap]
rs7002187	0.83[JPT][hapmap]
rs7002509	0.87[JPT][hapmap]
rs7009134	0.84[JPT][hapmap]
rs71525730	0.82[EUR][1000 genomes]
rs73196802	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73520657	0.96[ASN][1000 genomes]
rs73661775	0.89[AFR][1000 genomes]
rs7824209	0.89[JPT][hapmap]
rs7833479	0.81[AFR][1000 genomes]
rs7833481	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs7833484	0.81[AFR][1000 genomes]
rs894895	0.88[JPT][hapmap]
rs930557	0.94[JPT][hapmap]
rs963754	0.82[CHD][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv890056	chr8:6314486-6343727	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025860	chr8:6328628-6360743	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv890058	chr8:6329510-6367302	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17077109	AGPAT5	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
2	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
4	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
8	chr8:6308000-6372600	Weak transcription	HMEC	breast
9	chr8:6314400-6339600	Weak transcription	Brain Angular Gyrus	brain
10	chr8:6316400-6345600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:6317800-6380200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr8:6318400-6339600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:6318600-6339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr8:6321800-6342000	Weak transcription	Aorta	Aorta
15	chr8:6321800-6343800	Weak transcription	Hela-S3	cervix
16	chr8:6322000-6340000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:6322000-6346800	Weak transcription	Colon Smooth Muscle	Colon
18	chr8:6322200-6339800	Weak transcription	Psoas Muscle	Psoas
19	chr8:6323400-6339400	Weak transcription	Fetal Kidney	kidney
20	chr8:6323400-6339600	Weak transcription	A549	lung
21	chr8:6323400-6340200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:6323400-6342000	Weak transcription	NHEK	skin
23	chr8:6325800-6374400	Weak transcription	K562	blood
24	chr8:6326000-6340000	Weak transcription	Pancreas	Pancrea
25	chr8:6331400-6345600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr8:6333000-6342000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr8:6335000-6344200	Weak transcription	NHLF	lung
28	chr8:6335000-6345200	Weak transcription	Ovary	ovary
29	chr8:6335400-6341200	Weak transcription	Fetal Lung	lung
30	chr8:6335600-6344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr8:6336000-6340000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr8:6336800-6339600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr8:6336800-6340000	Weak transcription	HUVEC	blood vessel
34	chr8:6336800-6377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:6337000-6342200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:6337000-6342400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr8:6337200-6339400	Weak transcription	Fetal Brain Male	brain
38	chr8:6337600-6340400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr8:6337800-6339600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr8:6337800-6342200	Strong transcription	Lung	lung
41	chr8:6337800-6342400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr8:6337800-6347600	Strong transcription	Primary T cells from cord blood	blood
43	chr8:6338000-6339400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr8:6338000-6340800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr8:6338000-6342400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr8:6338000-6342400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:6338000-6342600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr8:6338000-6343600	Strong transcription	GM12878-XiMat	blood
49	chr8:6338200-6339600	Strong transcription	Fetal Muscle Leg	muscle
50	chr8:6338200-6339600	Enhancers	Osteobl	bone

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