Variant report

Variant	rs6138554
Chromosome Location	chr20:25242491-25242492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1046073	0.85[EUR][1000 genomes]
rs1077889	0.84[EUR][1000 genomes]
rs10966	0.83[EUR][1000 genomes]
rs11100	0.85[EUR][1000 genomes]
rs1118963	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1130694	0.84[EUR][1000 genomes]
rs11699953	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1555330	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1888997	0.83[EUR][1000 genomes]
rs1888998	0.86[EUR][1000 genomes]
rs1888999	0.86[EUR][1000 genomes]
rs2145126	0.86[EUR][1000 genomes]
rs2227890	0.86[EUR][1000 genomes]
rs2227892	0.86[EUR][1000 genomes]
rs2257233	0.86[EUR][1000 genomes]
rs2257420	0.85[EUR][1000 genomes]
rs2257432	0.85[EUR][1000 genomes]
rs2257461	0.86[EUR][1000 genomes]
rs2257464	0.85[EUR][1000 genomes]
rs2257496	0.85[EUR][1000 genomes]
rs2257705	0.86[EUR][1000 genomes]
rs2257712	0.86[EUR][1000 genomes]
rs2257808	0.85[EUR][1000 genomes]
rs2257809	0.85[EUR][1000 genomes]
rs2257982	0.85[EUR][1000 genomes]
rs2257985	0.85[EUR][1000 genomes]
rs2257988	0.85[EUR][1000 genomes]
rs2257991	0.85[EUR][1000 genomes]
rs2258066	0.85[EUR][1000 genomes]
rs2258135	0.84[EUR][1000 genomes]
rs2258201	0.85[EUR][1000 genomes]
rs2258563	0.85[EUR][1000 genomes]
rs2258617	0.85[EUR][1000 genomes]
rs2258719	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2258728	0.84[EUR][1000 genomes]
rs2258769	0.85[EUR][1000 genomes]
rs2258879	0.85[EUR][1000 genomes]
rs2258884	0.85[EUR][1000 genomes]
rs2259837	0.85[EUR][1000 genomes]
rs2259873	0.85[EUR][1000 genomes]
rs2259926	0.85[EUR][1000 genomes]
rs2259928	0.85[EUR][1000 genomes]
rs2259956	0.85[EUR][1000 genomes]
rs2260997	0.88[EUR][1000 genomes]
rs2261109	0.86[EUR][1000 genomes]
rs2261115	0.86[EUR][1000 genomes]
rs2261698	0.86[EUR][1000 genomes]
rs2261720	0.85[EUR][1000 genomes]
rs2261747	0.86[EUR][1000 genomes]
rs2261753	0.86[EUR][1000 genomes]
rs2261784	0.86[EUR][1000 genomes]
rs2261785	0.86[EUR][1000 genomes]
rs2261790	0.86[EUR][1000 genomes]
rs2261794	0.86[EUR][1000 genomes]
rs2261796	0.86[EUR][1000 genomes]
rs2297496	0.83[EUR][1000 genomes]
rs2297497	0.82[EUR][1000 genomes]
rs2424698	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424700	0.85[EUR][1000 genomes]
rs2424704	0.85[EUR][1000 genomes]
rs2424708	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2424710	0.86[EUR][1000 genomes]
rs2424711	0.86[EUR][1000 genomes]
rs2474766	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474769	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2474777	0.85[EUR][1000 genomes]
rs2482919	0.83[EUR][1000 genomes]
rs2482923	0.81[EUR][1000 genomes]
rs2482948	0.83[EUR][1000 genomes]
rs2500432	0.86[EUR][1000 genomes]
rs2500433	0.83[EUR][1000 genomes]
rs3002698	0.83[EUR][1000 genomes]
rs3002702	0.85[EUR][1000 genomes]
rs33999482	0.84[EUR][1000 genomes]
rs3746337	0.81[AMR][1000 genomes]
rs4355182	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4619688	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4813557	0.86[EUR][1000 genomes]
rs4815404	0.83[EUR][1000 genomes]
rs6037062	0.81[EUR][1000 genomes]
rs6037069	0.90[EUR][1000 genomes]
rs6037083	0.86[EUR][1000 genomes]
rs6037085	0.82[EUR][1000 genomes]
rs6037086	0.82[EUR][1000 genomes]
rs6050481	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050482	0.90[EUR][1000 genomes]
rs6050532	0.81[EUR][1000 genomes]
rs6107015	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6107017	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6107019	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6115093	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6115099	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6115100	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6115101	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6115109	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6115118	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6115140	0.86[EUR][1000 genomes]
rs6115146	0.82[EUR][1000 genomes]
rs6132819	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6132820	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132821	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6132822	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6132824	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6132826	0.85[EUR][1000 genomes]
rs6138545	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6138546	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6138550	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6138553	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6138555	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6138556	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66999585	0.83[EUR][1000 genomes]
rs7019	0.86[EUR][1000 genomes]
rs7020	0.84[EUR][1000 genomes]
rs7264176	0.83[EUR][1000 genomes]
rs7267979	0.82[EUR][1000 genomes]
rs7343481	0.82[EUR][1000 genomes]
rs7453	0.82[EUR][1000 genomes]
rs8184820	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs884613	0.86[EUR][1000 genomes]
rs910996	0.86[EUR][1000 genomes]
rs910997	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6138554	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138554	PYGB	cis	Whole Blood	GTEx
rs6138554	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138554	ABHD12	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25229800-25250000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:25231200-25251800	Weak transcription	Hela-S3	cervix
4	chr20:25231200-25252200	Weak transcription	HUVEC	blood vessel
5	chr20:25231400-25249800	Weak transcription	Small Intestine	intestine
6	chr20:25233200-25252200	Weak transcription	Fetal Brain Male	brain
7	chr20:25235000-25243000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
9	chr20:25236200-25243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr20:25236200-25251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr20:25236600-25253800	Weak transcription	Psoas Muscle	Psoas
12	chr20:25237600-25242800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr20:25237600-25243000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:25237600-25243000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr20:25237600-25249800	Weak transcription	NHDF-Ad	bronchial
16	chr20:25237600-25262800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:25238000-25249800	Weak transcription	Liver	Liver
18	chr20:25238000-25250000	Weak transcription	Placenta	Placenta
19	chr20:25238800-25242800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:25238800-25243000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:25238800-25243000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:25238800-25243600	Weak transcription	K562	blood
23	chr20:25239000-25243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:25239400-25242600	Strong transcription	Adipose Nuclei	Adipose
25	chr20:25239400-25242800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:25239400-25243400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr20:25239400-25243400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr20:25239600-25242600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:25239600-25242800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr20:25239600-25249800	Weak transcription	Pancreas	Pancrea
31	chr20:25239800-25249800	Weak transcription	Gastric	stomach
32	chr20:25240000-25243000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr20:25240600-25243000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:25240800-25249600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr20:25240800-25249600	Weak transcription	NHLF	lung
36	chr20:25240800-25249800	Weak transcription	Brain Anterior Caudate	brain
37	chr20:25240800-25249800	Weak transcription	Colon Smooth Muscle	Colon
38	chr20:25240800-25249800	Weak transcription	Ovary	ovary
39	chr20:25240800-25249800	Weak transcription	GM12878-XiMat	blood
40	chr20:25240800-25251400	Weak transcription	Thymus	Thymus
41	chr20:25241000-25242800	Enhancers	Primary T cells from cord blood	blood
42	chr20:25241000-25247400	Weak transcription	NH-A	brain
43	chr20:25241000-25249600	Weak transcription	NHEK	skin
44	chr20:25241000-25249800	Weak transcription	Fetal Heart	heart
45	chr20:25241000-25258200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr20:25241200-25246800	Weak transcription	HMEC	breast
47	chr20:25241400-25242800	Strong transcription	Colonic Mucosa	Colon
48	chr20:25241400-25242800	ZNF genes & repeats	Fetal Brain Female	brain
49	chr20:25241400-25243000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr20:25241400-25249200	Weak transcription	HSMM	muscle

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