Variant report

Variant	rs6138442
Chromosome Location	chr20:24960038-24960039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24959468..24961705-chr20:24961994..24965467,4	K562	blood:
2	chr20:24959038..24961782-chr20:24965978..24967936,3	MCF-7	breast:
3	chr20:24959138..24961345-chr20:25043562..25046337,2	MCF-7	breast:

Extended variants
information (count: 156 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056033	0.86[ASN][1000 genomes]
rs1056036	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11700073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11905625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11906373	0.93[ASN][1000 genomes]
rs12625319	0.84[ASN][1000 genomes]
rs13041643	0.86[ASN][1000 genomes]
rs1331286	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1535042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854849	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1977540	0.83[ASN][1000 genomes]
rs2008275	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2092565	0.86[ASN][1000 genomes]
rs2103736	0.86[ASN][1000 genomes]
rs2151462	0.93[ASN][1000 genomes]
rs2151463	0.93[ASN][1000 genomes]
rs2179729	0.86[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	0.86[ASN][1000 genomes]
rs2235847	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs227590	0.82[ASN][1000 genomes]
rs227598	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs227613	0.87[ASN][1000 genomes]
rs227614	0.90[ASN][1000 genomes]
rs227615	0.86[ASN][1000 genomes]
rs227616	0.93[ASN][1000 genomes]
rs227618	0.85[ASN][1000 genomes]
rs227619	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227620	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227621	0.93[ASN][1000 genomes]
rs227622	0.93[ASN][1000 genomes]
rs227623	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227624	0.93[ASN][1000 genomes]
rs227625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs227626	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227627	0.90[ASN][1000 genomes]
rs227628	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227629	0.93[ASN][1000 genomes]
rs227630	0.93[ASN][1000 genomes]
rs227631	0.93[ASN][1000 genomes]
rs227632	0.93[ASN][1000 genomes]
rs227633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227635	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227639	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227643	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227646	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227648	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227649	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs227650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227651	0.93[ASN][1000 genomes]
rs227652	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227657	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227658	0.93[ASN][1000 genomes]
rs227659	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2387365	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2387366	0.86[ASN][1000 genomes]
rs2387572	0.86[ASN][1000 genomes]
rs2424691	0.93[ASN][1000 genomes]
rs2892279	0.88[ASN][1000 genomes]
rs34419834	0.86[ASN][1000 genomes]
rs3746330	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4273288	0.83[ASN][1000 genomes]
rs4527284	0.80[ASN][1000 genomes]
rs4539860	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45468392	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45556041	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813541	0.86[ASN][1000 genomes]
rs4813542	0.86[ASN][1000 genomes]
rs4815327	0.83[ASN][1000 genomes]
rs4815337	0.86[ASN][1000 genomes]
rs4815339	0.84[ASN][1000 genomes]
rs4815340	0.86[ASN][1000 genomes]
rs4815341	0.88[ASN][1000 genomes]
rs4815351	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4815355	0.86[ASN][1000 genomes]
rs4815357	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56312312	0.97[ASN][1000 genomes]
rs57265446	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58244398	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036976	0.83[ASN][1000 genomes]
rs6050118	0.80[AMR][1000 genomes]
rs6050131	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050134	0.89[AMR][1000 genomes];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[JPT][hapmap];0.88[ASN][1000 genomes]
rs6050249	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6050255	0.86[JPT][hapmap]
rs6050259	0.86[JPT][hapmap]
rs6050261	0.86[JPT][hapmap]
rs6083684	0.86[ASN][1000 genomes]
rs6083685	0.86[ASN][1000 genomes]
rs6083686	0.86[ASN][1000 genomes]
rs6083688	0.86[ASN][1000 genomes]
rs6083692	0.84[ASN][1000 genomes]
rs6083699	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6083709	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6106975	0.88[ASN][1000 genomes]
rs6106984	0.97[ASN][1000 genomes]
rs6114980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6114981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6114984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6114988	0.97[ASN][1000 genomes]
rs6132773	0.86[ASN][1000 genomes]
rs6132774	0.86[ASN][1000 genomes]
rs6132775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132784	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6132789	0.86[JPT][hapmap]
rs6138417	0.86[ASN][1000 genomes]
rs6138423	0.86[ASN][1000 genomes]
rs6138431	0.80[ASN][1000 genomes]
rs6138435	0.86[ASN][1000 genomes]
rs6138437	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6138438	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138453	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138456	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6138460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138461	0.85[ASN][1000 genomes]
rs6138463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138465	0.81[ASN][1000 genomes]
rs6138466	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138473	0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.86[JPT][hapmap]
rs62215110	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215115	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62215128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215131	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7268095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7269416	0.97[ASN][1000 genomes]
rs735886	0.86[ASN][1000 genomes]
rs8125909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8183891	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs914314	0.85[ASN][1000 genomes]
rs926661	0.88[ASN][1000 genomes]
rs926662	0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6138442	CST7	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24935200-24971800	Weak transcription	K562	blood
2	chr20:24942000-24972400	Weak transcription	Fetal Heart	heart
3	chr20:24942800-24961600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr20:24943200-24965000	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr20:24944800-24960600	Weak transcription	Stomach Mucosa	stomach
6	chr20:24950000-24966400	Weak transcription	Small Intestine	intestine
7	chr20:24950800-24961000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:24951600-24960400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
9	chr20:24952800-24961000	Weak transcription	NHDF-Ad	bronchial
10	chr20:24953200-24962200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr20:24953600-24960400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:24953600-24960800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr20:24953600-24972000	Weak transcription	NH-A	brain
14	chr20:24954000-24960600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr20:24954000-24961000	Weak transcription	Colon Smooth Muscle	Colon
16	chr20:24954200-24960800	Weak transcription	HMEC	breast
17	chr20:24954200-24960800	Weak transcription	NHEK	skin
18	chr20:24954200-24961000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr20:24954200-24961000	Weak transcription	HSMMtube	muscle
20	chr20:24954200-24961800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr20:24954200-24965800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr20:24954400-24961000	Weak transcription	NHLF	lung
23	chr20:24954800-24961200	Weak transcription	Right Ventricle	heart
24	chr20:24954800-24965800	Weak transcription	Psoas Muscle	Psoas
25	chr20:24955400-24961200	Weak transcription	Hela-S3	cervix
26	chr20:24956400-24960600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr20:24956800-24962000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr20:24957000-24960200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr20:24957000-24960200	Strong transcription	Fetal Intestine Large	intestine
30	chr20:24957000-24960400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr20:24957000-24961200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr20:24957000-24962800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr20:24957000-24963200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:24957000-24963600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr20:24957000-24964200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr20:24957200-24960400	Strong transcription	Placenta	Placenta
37	chr20:24957200-24961000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr20:24957200-24961600	Strong transcription	Aorta	Aorta
39	chr20:24957200-24962000	Genic enhancers	Brain Hippocampus Middle	brain
40	chr20:24957200-24963800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:24957200-24964600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr20:24957400-24961200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr20:24957400-24963200	Strong transcription	Spleen	Spleen
44	chr20:24957600-24960200	Strong transcription	Primary B cells from cord blood	blood
45	chr20:24957600-24962800	Genic enhancers	Liver	Liver
46	chr20:24957600-24963000	Genic enhancers	Adipose Nuclei	Adipose
47	chr20:24957600-24963000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr20:24957600-24964200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:24957600-24965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr20:24957800-24960200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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