Variant report

Variant	rs6050757
Chromosome Location	chr20:25629800-25629801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 186 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:185)

rs_ID	r²[population]
rs10485776	1.00[JPT][hapmap]
rs11087521	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1109100	1.00[JPT][hapmap]
rs1122769	1.00[JPT][hapmap]
rs11699203	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12106173	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12428	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1569617	1.00[JPT][hapmap]
rs16987767	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs16987786	1.00[JPT][hapmap]
rs16987789	1.00[JPT][hapmap]
rs16987799	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs16987820	1.00[JPT][hapmap]
rs16987934	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs16988014	1.00[JPT][hapmap]
rs1883528	1.00[JPT][hapmap]
rs2103661	0.85[JPT][hapmap]
rs2179458	1.00[JPT][hapmap]
rs2387977	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2388026	0.84[ASN][1000 genomes]
rs242130	0.81[CHD][hapmap]
rs242133	1.00[JPT][hapmap]
rs2424719	1.00[JPT][hapmap]
rs2856	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs372678	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3764695	0.84[ASN][1000 genomes]
rs3813916	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs397119	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs398036	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs401166	1.00[JPT][hapmap]
rs402120	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4098823	0.84[ASN][1000 genomes]
rs4098824	0.84[ASN][1000 genomes]
rs4113658	0.84[ASN][1000 genomes]
rs4113659	0.84[ASN][1000 genomes]
rs4113661	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4113662	0.84[ASN][1000 genomes]
rs417110	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs417130	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs422844	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs424487	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs426563	1.00[JPT][hapmap]
rs428278	1.00[JPT][hapmap]
rs431579	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4318454	0.81[ASN][1000 genomes]
rs433352	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4343537	0.84[ASN][1000 genomes]
rs4368405	0.81[ASN][1000 genomes]
rs437635	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs442834	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs446649	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs447808	1.00[JPT][hapmap]
rs449370	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs449703	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs454723	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4574179	0.84[ASN][1000 genomes]
rs4813579	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815436	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4815438	0.89[LWK][hapmap]
rs4815445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815450	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57638633	0.84[ASN][1000 genomes]
rs59399848	0.81[ASN][1000 genomes]
rs6037128	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6037131	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6037133	1.00[JPT][hapmap]
rs6037159	1.00[JPT][hapmap]
rs6037161	1.00[JPT][hapmap]
rs6037164	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6037166	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6037167	1.00[JPT][hapmap]
rs6037169	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6037179	0.84[ASN][1000 genomes]
rs6037180	0.84[ASN][1000 genomes]
rs6037193	0.84[ASN][1000 genomes]
rs6037195	0.82[JPT][hapmap]
rs6037196	1.00[JPT][hapmap]
rs6037198	0.84[ASN][1000 genomes]
rs6037199	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6037206	0.81[ASN][1000 genomes]
rs6037208	0.84[ASN][1000 genomes]
rs6037212	0.84[ASN][1000 genomes]
rs6037217	0.84[ASN][1000 genomes]
rs6037220	0.84[ASN][1000 genomes]
rs6037222	0.82[JPT][hapmap]
rs6037223	1.00[JPT][hapmap]
rs60463280	0.81[ASN][1000 genomes]
rs6050663	1.00[JPT][hapmap]
rs6050710	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050712	1.00[JPT][hapmap]
rs6050717	1.00[JPT][hapmap]
rs6050724	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050725	1.00[JPT][hapmap]
rs6050726	1.00[JPT][hapmap]
rs6050732	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050733	1.00[JPT][hapmap]
rs6050745	0.84[ASN][1000 genomes]
rs6050749	0.84[ASN][1000 genomes]
rs6050753	0.84[ASN][1000 genomes]
rs6050754	0.84[ASN][1000 genomes]
rs6050755	0.84[ASN][1000 genomes]
rs6050756	0.84[ASN][1000 genomes]
rs6050758	0.84[ASN][1000 genomes]
rs6050760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050765	0.84[ASN][1000 genomes]
rs6050767	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050768	0.84[ASN][1000 genomes]
rs6050770	0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050775	0.84[ASN][1000 genomes]
rs6050779	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050787	0.84[ASN][1000 genomes]
rs6050788	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050789	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050791	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6050795	0.84[ASN][1000 genomes]
rs6050796	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050799	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050801	0.81[ASN][1000 genomes]
rs6050802	0.84[ASN][1000 genomes]
rs6050804	0.84[ASN][1000 genomes]
rs6050805	0.81[ASN][1000 genomes]
rs6050807	0.81[ASN][1000 genomes]
rs6050809	0.84[ASN][1000 genomes]
rs6050832	0.84[ASN][1000 genomes]
rs6050833	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050834	0.84[ASN][1000 genomes]
rs6050835	0.84[ASN][1000 genomes]
rs6050838	0.84[ASN][1000 genomes]
rs6050840	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050841	0.84[ASN][1000 genomes]
rs6050846	0.84[ASN][1000 genomes]
rs6050847	0.84[ASN][1000 genomes]
rs6050848	0.84[ASN][1000 genomes]
rs6050851	0.84[ASN][1000 genomes]
rs6050853	0.84[ASN][1000 genomes]
rs6050854	0.84[ASN][1000 genomes]
rs6050858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050867	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083886	1.00[JPT][hapmap]
rs6083896	1.00[JPT][hapmap]
rs6083897	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs6083899	1.00[JPT][hapmap]
rs61052177	0.81[ASN][1000 genomes]
rs6107045	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6107047	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6115191	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6115200	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6115214	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6115215	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6115224	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6115232	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132848	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132850	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6138572	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138575	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6138588	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6138600	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138612	1.00[JPT][hapmap]
rs7266130	1.00[JPT][hapmap]
rs7266592	1.00[JPT][hapmap]
rs7270835	1.00[JPT][hapmap]
rs73341361	0.84[ASN][1000 genomes]
rs73341363	0.81[ASN][1000 genomes]
rs73341365	0.81[ASN][1000 genomes]
rs73341397	0.84[ASN][1000 genomes]
rs73343217	0.84[ASN][1000 genomes]
rs73343255	0.84[ASN][1000 genomes]
rs73343275	0.81[ASN][1000 genomes]
rs73343292	0.81[ASN][1000 genomes]
rs73345232	0.84[ASN][1000 genomes]
rs7346687	0.84[ASN][1000 genomes]
rs742435	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs8115742	1.00[JPT][hapmap]
rs8116267	1.00[JPT][hapmap]
rs8117181	1.00[JPT][hapmap]
rs8120065	1.00[JPT][hapmap]
rs8120594	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs8121648	1.00[JPT][hapmap]
rs84816	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs926486	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926487	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs928121	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9753575	0.84[ASN][1000 genomes]
rs981440	0.84[ASN][1000 genomes]
rs981441	0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6050757	NANP	cis	cerebellum	SCAN
rs6050757	ZNF337	cis	Thyroid	GTEx
rs6050757	RP4-694B14.5	cis	Thyroid	GTEx
rs6050757	RP4-694B14.5	cis	lung	GTEx
rs6050757	ZNF337	cis	cerebellum	SCAN
rs6050757	VSX1	cis	cerebellum	SCAN
rs6050757	CST2	cis	parietal	SCAN
rs6050757	ENTPD6	cis	parietal	SCAN
rs6050757	NINL	cis	Nerve Tibial	GTEx
rs6050757	ZNF337	cis	lymphoblastoid	seeQTL
rs6050757	ZNF337	cis	Stomach	GTEx
rs6050757	ZNF337	cis	lung	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25605400-25630400	Weak transcription	Aorta	Aorta
2	chr20:25605600-25630200	Weak transcription	Fetal Intestine Large	intestine
3	chr20:25605600-25635000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr20:25605600-25654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr20:25609200-25653400	Weak transcription	Brain Substantia Nigra	brain
6	chr20:25610200-25630400	Weak transcription	Ovary	ovary
7	chr20:25610200-25635600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:25610600-25630600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr20:25611400-25653200	Weak transcription	Fetal Intestine Small	intestine
10	chr20:25613400-25635000	Weak transcription	Hela-S3	cervix
11	chr20:25613600-25635400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:25614400-25632400	Weak transcription	Osteobl	bone
13	chr20:25614600-25635000	Weak transcription	NHEK	skin
14	chr20:25616000-25653600	Weak transcription	Adipose Nuclei	Adipose
15	chr20:25617000-25650400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr20:25617400-25640400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr20:25617600-25653400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr20:25617800-25635000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:25618400-25632200	Weak transcription	Primary T cells from cord blood	blood
20	chr20:25618400-25653600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr20:25618400-25653600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr20:25623200-25653600	Weak transcription	Pancreas	Pancrea
23	chr20:25624000-25635400	Weak transcription	HepG2	liver
24	chr20:25624200-25630000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:25624800-25629800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr20:25624800-25631800	Weak transcription	GM12878-XiMat	blood
27	chr20:25625000-25655200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr20:25625200-25641600	Weak transcription	Dnd41	blood
29	chr20:25625600-25630400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr20:25626400-25630000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr20:25626400-25653600	Weak transcription	Fetal Muscle Leg	muscle
32	chr20:25626800-25632400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr20:25626800-25634800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:25626800-25654000	Weak transcription	Gastric	stomach
35	chr20:25627000-25632600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr20:25627400-25640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:25628200-25653600	Weak transcription	Esophagus	oesophagus
38	chr20:25628600-25636600	Weak transcription	A549	lung
39	chr20:25628800-25630600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr20:25628800-25631400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr20:25628800-25640600	Weak transcription	Fetal Thymus	thymus
42	chr20:25628800-25653400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr20:25628800-25653400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr20:25628800-25653400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr20:25629000-25635000	Weak transcription	HSMMtube	muscle
46	chr20:25629000-25649000	Weak transcription	Thymus	Thymus
47	chr20:25629000-25649200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr20:25629000-25652200	Weak transcription	Liver	Liver
49	chr20:25629000-25653400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr20:25629000-25653600	Weak transcription	Brain Hippocampus Middle	brain

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