Variant report

Variant	rs6050833
Chromosome Location	chr20:25699264-25699265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs2388026	0.86[ASN][1000 genomes]
rs35516971	0.81[ASN][1000 genomes]
rs3764695	0.86[ASN][1000 genomes]
rs3813916	0.84[ASN][1000 genomes]
rs4098823	0.86[ASN][1000 genomes]
rs4098824	0.86[ASN][1000 genomes]
rs4113658	0.86[ASN][1000 genomes]
rs4113659	0.86[ASN][1000 genomes]
rs4113661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113662	0.86[ASN][1000 genomes]
rs41308623	0.81[ASN][1000 genomes]
rs4318454	0.84[ASN][1000 genomes]
rs4343537	0.86[ASN][1000 genomes]
rs4368405	0.84[ASN][1000 genomes]
rs4574179	0.86[ASN][1000 genomes]
rs4813579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815445	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815450	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57638633	0.86[ASN][1000 genomes]
rs59399848	0.84[ASN][1000 genomes]
rs6037159	0.81[ASN][1000 genomes]
rs6037161	0.81[ASN][1000 genomes]
rs6037164	0.81[ASN][1000 genomes]
rs6037167	0.81[ASN][1000 genomes]
rs6037168	0.81[ASN][1000 genomes]
rs6037169	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6037179	0.86[ASN][1000 genomes]
rs6037180	0.86[ASN][1000 genomes]
rs6037193	0.86[ASN][1000 genomes]
rs6037198	0.86[ASN][1000 genomes]
rs6037199	0.86[ASN][1000 genomes]
rs6037204	0.81[ASN][1000 genomes]
rs6037206	0.84[ASN][1000 genomes]
rs6037208	0.86[ASN][1000 genomes]
rs6037212	0.86[ASN][1000 genomes]
rs6037217	0.86[ASN][1000 genomes]
rs6037220	0.86[ASN][1000 genomes]
rs6037223	0.81[ASN][1000 genomes]
rs60463280	0.84[ASN][1000 genomes]
rs6050707	0.81[ASN][1000 genomes]
rs6050709	0.81[ASN][1000 genomes]
rs6050710	0.81[ASN][1000 genomes]
rs6050712	0.81[ASN][1000 genomes]
rs6050714	0.81[ASN][1000 genomes]
rs6050717	0.81[ASN][1000 genomes]
rs6050720	0.81[ASN][1000 genomes]
rs6050723	0.81[ASN][1000 genomes]
rs6050724	0.81[ASN][1000 genomes]
rs6050725	0.81[ASN][1000 genomes]
rs6050726	0.81[ASN][1000 genomes]
rs6050727	0.81[ASN][1000 genomes]
rs6050729	0.81[ASN][1000 genomes]
rs6050730	0.81[ASN][1000 genomes]
rs6050732	0.81[ASN][1000 genomes]
rs6050733	0.81[ASN][1000 genomes]
rs6050737	0.81[ASN][1000 genomes]
rs6050743	0.81[ASN][1000 genomes]
rs6050745	0.86[ASN][1000 genomes]
rs6050749	0.86[ASN][1000 genomes]
rs6050753	0.86[ASN][1000 genomes]
rs6050754	0.86[ASN][1000 genomes]
rs6050755	0.86[ASN][1000 genomes]
rs6050756	0.86[ASN][1000 genomes]
rs6050757	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050758	0.86[ASN][1000 genomes]
rs6050760	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050763	0.81[ASN][1000 genomes]
rs6050765	0.86[ASN][1000 genomes]
rs6050767	0.84[ASN][1000 genomes]
rs6050768	0.86[ASN][1000 genomes]
rs6050770	0.84[ASN][1000 genomes]
rs6050775	0.86[ASN][1000 genomes]
rs6050779	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050787	0.86[ASN][1000 genomes]
rs6050788	0.86[ASN][1000 genomes]
rs6050789	0.86[ASN][1000 genomes]
rs6050791	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050795	0.86[ASN][1000 genomes]
rs6050796	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050799	0.86[ASN][1000 genomes]
rs6050801	0.84[ASN][1000 genomes]
rs6050802	0.86[ASN][1000 genomes]
rs6050804	0.86[ASN][1000 genomes]
rs6050805	0.84[ASN][1000 genomes]
rs6050807	0.84[ASN][1000 genomes]
rs6050809	0.86[ASN][1000 genomes]
rs6050814	0.83[AFR][1000 genomes]
rs6050832	0.86[ASN][1000 genomes]
rs6050834	0.86[ASN][1000 genomes]
rs6050835	0.86[ASN][1000 genomes]
rs6050838	0.86[ASN][1000 genomes]
rs6050840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050841	0.86[ASN][1000 genomes]
rs6050846	0.86[ASN][1000 genomes]
rs6050847	0.86[ASN][1000 genomes]
rs6050848	0.86[ASN][1000 genomes]
rs6050851	0.86[ASN][1000 genomes]
rs6050853	0.86[ASN][1000 genomes]
rs6050854	0.86[ASN][1000 genomes]
rs6050858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050867	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61052177	0.84[ASN][1000 genomes]
rs6115232	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73341361	0.86[ASN][1000 genomes]
rs73341363	0.84[ASN][1000 genomes]
rs73341365	0.84[ASN][1000 genomes]
rs73341397	0.86[ASN][1000 genomes]
rs73343217	0.86[ASN][1000 genomes]
rs73343255	0.86[ASN][1000 genomes]
rs73343275	0.84[ASN][1000 genomes]
rs73343292	0.84[ASN][1000 genomes]
rs73345232	0.86[ASN][1000 genomes]
rs7346687	0.86[ASN][1000 genomes]
rs8120065	0.81[ASN][1000 genomes]
rs8120594	0.81[ASN][1000 genomes]
rs8121013	0.81[ASN][1000 genomes]
rs8126236	0.81[ASN][1000 genomes]
rs926486	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926487	0.86[ASN][1000 genomes]
rs9753575	0.86[ASN][1000 genomes]
rs981440	0.86[ASN][1000 genomes]
rs981441	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv525033	chr20:25688001-25730968	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3451414	chr20:25696452-25700550	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	esv17092	chr20:25698651-25707971	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
7	esv3411467	chr20:25698707-25700769	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6050833	ZNF337	cis	Stomach	GTEx
rs6050833	RP4-694B14.5	cis	Thyroid	GTEx
rs6050833	ZNF337	cis	Thyroid	GTEx
rs6050833	ZNF337	cis	lung	GTEx
rs6050833	RP4-694B14.5	cis	lung	GTEx
rs6050833	NINL	cis	Nerve Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25677800-25701000	Weak transcription	Pancreas	Pancrea
2	chr20:25694000-25700200	Weak transcription	Primary T cells from cord blood	blood
3	chr20:25694200-25705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr20:25697800-25700000	Weak transcription	Gastric	stomach
5	chr20:25698600-25700600	Weak transcription	Ovary	ovary
6	chr20:25699200-25700800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr20:25699200-25701200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr20:25699200-25701200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr20:25699200-25701200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr20:25699200-25701400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr20:25699200-25701400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr20:25699200-25701400	Weak transcription	Brain Hippocampus Middle	brain

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