Variant report

Variant	rs6707
Chromosome Location	chr20:24944166-24944167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 159 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.91[ASN][1000 genomes]
rs1056036	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11700073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11905625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11906373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12625319	0.89[ASN][1000 genomes]
rs13041643	0.91[ASN][1000 genomes]
rs1331286	0.86[ASN][1000 genomes]
rs1535042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1854849	0.86[ASN][1000 genomes]
rs1977540	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2008275	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2092565	0.91[ASN][1000 genomes]
rs2103736	0.91[ASN][1000 genomes]
rs2151462	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151463	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179729	0.91[ASN][1000 genomes]
rs2179730	0.88[ASN][1000 genomes]
rs2179732	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2206891	0.82[ASN][1000 genomes]
rs2225459	0.91[ASN][1000 genomes]
rs2235847	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs227590	0.88[ASN][1000 genomes]
rs227597	0.85[ASN][1000 genomes]
rs227598	0.83[ASN][1000 genomes]
rs227609	0.81[ASN][1000 genomes]
rs227613	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs227614	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227615	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227616	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227618	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227619	0.95[ASN][1000 genomes]
rs227620	0.95[ASN][1000 genomes]
rs227621	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227622	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227623	0.95[ASN][1000 genomes]
rs227624	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227626	0.95[ASN][1000 genomes]
rs227627	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227628	0.95[ASN][1000 genomes]
rs227629	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227630	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227631	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227632	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227633	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs227634	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs227635	0.95[ASN][1000 genomes]
rs227639	0.95[ASN][1000 genomes]
rs227643	0.95[ASN][1000 genomes]
rs227646	0.95[ASN][1000 genomes]
rs227648	0.95[ASN][1000 genomes]
rs227649	0.85[ASN][1000 genomes]
rs227650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs227651	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227652	0.95[ASN][1000 genomes]
rs227653	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs227657	0.95[ASN][1000 genomes]
rs227658	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227659	0.95[ASN][1000 genomes]
rs2387365	0.86[ASN][1000 genomes]
rs2387366	0.91[ASN][1000 genomes]
rs2387572	0.91[ASN][1000 genomes]
rs2424691	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2892279	0.88[ASN][1000 genomes]
rs34419834	0.91[ASN][1000 genomes]
rs3746330	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs4273288	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4462848	0.82[EUR][1000 genomes]
rs4527284	0.85[ASN][1000 genomes]
rs4539860	0.90[ASN][1000 genomes]
rs45468392	0.95[ASN][1000 genomes]
rs45556041	0.95[ASN][1000 genomes]
rs4594518	0.82[ASN][1000 genomes]
rs4813541	0.91[ASN][1000 genomes]
rs4813542	0.91[ASN][1000 genomes]
rs4815325	0.83[EUR][1000 genomes]
rs4815327	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4815337	0.91[ASN][1000 genomes]
rs4815339	0.89[ASN][1000 genomes]
rs4815340	0.91[ASN][1000 genomes]
rs4815341	0.88[ASN][1000 genomes]
rs4815351	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4815355	0.91[ASN][1000 genomes]
rs4815357	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs56312312	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57265446	0.88[ASN][1000 genomes]
rs58244398	0.90[ASN][1000 genomes]
rs6036976	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6050131	0.81[ASN][1000 genomes]
rs6050134	0.86[ASN][1000 genomes]
rs6050177	0.88[ASN][1000 genomes]
rs6050179	0.88[ASN][1000 genomes]
rs6050181	0.88[ASN][1000 genomes]
rs6050198	0.85[CHB][hapmap]
rs6050201	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6050249	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6050255	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050259	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050261	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6083684	0.91[ASN][1000 genomes]
rs6083685	0.91[ASN][1000 genomes]
rs6083686	0.91[ASN][1000 genomes]
rs6083688	0.91[ASN][1000 genomes]
rs6083692	0.89[ASN][1000 genomes]
rs6083699	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6083709	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6106975	0.88[ASN][1000 genomes]
rs6106984	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114988	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132773	0.91[ASN][1000 genomes]
rs6132774	0.91[ASN][1000 genomes]
rs6132775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6132777	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6132778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6132783	0.84[ASN][1000 genomes]
rs6132784	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6132789	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138406	0.82[ASN][1000 genomes]
rs6138417	0.91[ASN][1000 genomes]
rs6138423	0.91[ASN][1000 genomes]
rs6138431	0.85[ASN][1000 genomes]
rs6138435	0.91[ASN][1000 genomes]
rs6138437	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138438	0.95[ASN][1000 genomes]
rs6138442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6138453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6138455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6138456	0.90[ASN][1000 genomes]
rs6138457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6138458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138460	0.84[ASN][1000 genomes]
rs6138461	0.80[ASN][1000 genomes]
rs6138466	0.82[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6138473	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs62215110	0.95[ASN][1000 genomes]
rs62215115	0.95[ASN][1000 genomes]
rs62215128	0.90[ASN][1000 genomes]
rs62215131	0.90[ASN][1000 genomes]
rs7268095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7269416	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735886	0.91[ASN][1000 genomes]
rs8125909	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8183891	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs914314	0.86[ASN][1000 genomes]
rs926661	0.88[ASN][1000 genomes]
rs926662	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6707	CST9	cis	parietal	SCAN
rs6707	PYGB	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24935000-24953600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr20:24935200-24957600	Strong transcription	Liver	Liver
3	chr20:24935200-24971800	Weak transcription	K562	blood
4	chr20:24935800-24945200	Strong transcription	Skeletal Muscle Male	skeletal muscle
5	chr20:24936000-24955600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr20:24936200-24947400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr20:24936200-24954400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:24936400-24947000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr20:24936400-24954400	Strong transcription	Fetal Intestine Small	intestine
10	chr20:24936400-24954400	Strong transcription	Fetal Stomach	stomach
11	chr20:24936400-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:24936400-24954600	Strong transcription	Brain Germinal Matrix	brain
13	chr20:24936400-24954600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr20:24936400-24954800	Strong transcription	Spleen	Spleen
15	chr20:24936400-24956000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr20:24936600-24944200	Strong transcription	Fetal Muscle Leg	muscle
17	chr20:24936600-24944400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr20:24936600-24945800	Strong transcription	Brain Hippocampus Middle	brain
19	chr20:24936600-24947200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:24936600-24950600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr20:24936600-24954200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:24936600-24954200	Strong transcription	Brain Substantia Nigra	brain
23	chr20:24936600-24954200	Strong transcription	Gastric	stomach
24	chr20:24936600-24954800	Strong transcription	Brain Anterior Caudate	brain
25	chr20:24936600-24954800	Strong transcription	Thymus	Thymus
26	chr20:24936800-24952600	Strong transcription	Placenta	Placenta
27	chr20:24936800-24954800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr20:24936800-24955000	Strong transcription	Lung	lung
29	chr20:24936800-24955400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr20:24936800-24955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr20:24937000-24945400	Strong transcription	Fetal Brain Female	brain
32	chr20:24937000-24950600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr20:24937000-24955000	Strong transcription	Dnd41	blood
34	chr20:24937200-24954400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr20:24937200-24954400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr20:24937200-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr20:24937200-24954800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr20:24937200-24955000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr20:24937400-24954200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr20:24937400-24957200	Strong transcription	HepG2	liver
41	chr20:24937600-24954600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:24937800-24945200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr20:24937800-24954400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr20:24937800-24954800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:24937800-24955000	Strong transcription	Primary T cells from cord blood	blood
46	chr20:24938000-24948000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr20:24938000-24954600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr20:24938000-24954800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr20:24938000-24954800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr20:24938200-24954200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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