Variant report

Variant	rs6138569
Chromosome Location	chr20:25425808-25425809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11699872	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12480853	0.84[JPT][hapmap]
rs2072975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2227891	1.00[ASW][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]
rs2228976	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2235605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236180	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257370	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs2258053	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2261177	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2263205	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2281559	1.00[ASW][hapmap];0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2294583	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424701	1.00[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs2424705	0.81[AMR][1000 genomes]
rs2424707	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2482908	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2482933	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2482934	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2482938	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2482947	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2500395	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2500403	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2500441	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2500442	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3787078	1.00[ASW][hapmap];0.86[CEU][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs3787081	1.00[ASW][hapmap];0.86[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs59046052	0.88[AMR][1000 genomes]
rs6050603	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6050690	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6115218	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6132842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs6132851	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6138573	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6138576	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138580	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138584	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138595	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6138598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6138599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6138601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6138604	0.93[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes]
rs6138611	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6138616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes]
rs6138622	0.88[AMR][1000 genomes]
rs6138623	0.88[AMR][1000 genomes]
rs6138625	0.82[AMR][1000 genomes]
rs723774	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878176	0.91[CEU][hapmap];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription 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 target site	21 gene(s)	inside rSNPs	diseases
14	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
16	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv1059494	chr20:25377602-25441835	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
20	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6138569	NXT1	cis	cerebellum	SCAN
rs6138569	C20orf22	cis	multi-tissue	Pritchard
rs6138569	PYGB	cis	multi-tissue	Pritchard
rs6138569	ABHD12	cis	lymphoblastoid	seeQTL
rs6138569	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138569	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138569	PYGB	cis	Whole Blood	GTEx
rs6138569	DCLRE1C	trans	multi-tissue	Pritchard
rs6138569	HDHD4	cis	multi-tissue	Pritchard
rs6138569	NINL	cis	parietal	SCAN
rs6138569	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6138569	GINS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25389000-25433600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:25389600-25426400	Weak transcription	NH-A	brain
3	chr20:25389600-25426600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr20:25389600-25432200	Weak transcription	Fetal Brain Male	brain
5	chr20:25389800-25432600	Weak transcription	Esophagus	oesophagus
6	chr20:25390000-25434800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr20:25390600-25426200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr20:25390600-25433400	Weak transcription	Brain Germinal Matrix	brain
9	chr20:25392200-25430800	Strong transcription	Dnd41	blood
10	chr20:25398800-25429800	Weak transcription	Hela-S3	cervix
11	chr20:25399800-25433600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:25399800-25434800	Weak transcription	NHLF	lung
13	chr20:25402800-25445200	Weak transcription	NHDF-Ad	bronchial
14	chr20:25406000-25432600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:25406800-25426600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:25409000-25427000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr20:25409000-25432800	Weak transcription	K562	blood
18	chr20:25412000-25426600	Weak transcription	Fetal Kidney	kidney
19	chr20:25412000-25429000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:25412200-25433600	Weak transcription	Spleen	Spleen
21	chr20:25412400-25432200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr20:25412600-25428400	Weak transcription	Fetal Brain Female	brain
23	chr20:25412600-25440200	Weak transcription	Placenta	Placenta
24	chr20:25413800-25430600	Weak transcription	Aorta	Aorta
25	chr20:25414200-25436000	Weak transcription	Primary T cells from cord blood	blood
26	chr20:25415400-25433600	Weak transcription	Pancreas	Pancrea
27	chr20:25415600-25432200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr20:25415600-25432400	Weak transcription	Ovary	ovary
29	chr20:25416000-25426800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:25416000-25429200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:25418200-25428800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr20:25418200-25429200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr20:25418200-25429800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:25418200-25430400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr20:25418200-25431600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr20:25418200-25432600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr20:25418200-25434800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr20:25418200-25436600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr20:25418200-25445200	Weak transcription	HSMM	muscle
40	chr20:25418400-25429200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr20:25418400-25429400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr20:25418400-25429600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr20:25418400-25430000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr20:25418400-25430400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr20:25418400-25432400	Weak transcription	Fetal Heart	heart
46	chr20:25418400-25433600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr20:25418800-25431000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:25418800-25439400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:25419000-25431400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr20:25419600-25426400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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