Variant report

Variant	rs6050841
Chromosome Location	chr20:25701470-25701471
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 211 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:206)

rs_ID	r²[population]
rs10485776	0.89[EUR][1000 genomes]
rs1109100	0.89[EUR][1000 genomes]
rs1122769	0.93[EUR][1000 genomes]
rs12106173	0.95[EUR][1000 genomes]
rs1569617	0.91[ASN][1000 genomes]
rs16987799	0.89[EUR][1000 genomes]
rs16987820	0.89[EUR][1000 genomes]
rs16987934	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16988014	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1891771	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1936188	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1936190	0.82[EUR][1000 genomes]
rs2103661	0.85[ASN][1000 genomes]
rs2179458	0.89[EUR][1000 genomes]
rs2388026	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242130	0.88[ASN][1000 genomes]
rs242133	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35516971	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3764695	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813916	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs400070	0.89[EUR][1000 genomes]
rs402120	0.87[EUR][1000 genomes]
rs409322	0.83[EUR][1000 genomes]
rs409401	0.87[EUR][1000 genomes]
rs4098823	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4098824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113661	0.86[ASN][1000 genomes]
rs4113662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308623	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4318454	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4343537	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368405	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs440612	0.89[EUR][1000 genomes]
rs447808	0.87[EUR][1000 genomes]
rs4574179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813570	0.89[EUR][1000 genomes]
rs4813579	0.86[ASN][1000 genomes]
rs4815445	0.86[ASN][1000 genomes]
rs4815450	0.86[ASN][1000 genomes]
rs57638633	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58169034	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59324912	0.89[EUR][1000 genomes]
rs59399848	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59546510	0.89[EUR][1000 genomes]
rs6037131	0.89[EUR][1000 genomes]
rs6037133	0.89[EUR][1000 genomes]
rs6037159	0.94[ASN][1000 genomes]
rs6037161	0.94[ASN][1000 genomes]
rs6037164	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6037166	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6037167	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6037168	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6037179	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037180	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037192	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6037193	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037195	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6037196	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6037198	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037199	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037204	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6037205	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6037206	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6037208	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037212	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037217	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037220	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037222	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6037223	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60394570	0.80[ASN][1000 genomes]
rs60463280	0.97[ASN][1000 genomes]
rs6050658	0.89[EUR][1000 genomes]
rs6050663	0.89[EUR][1000 genomes]
rs6050692	0.82[ASN][1000 genomes]
rs6050707	0.94[ASN][1000 genomes]
rs6050709	0.94[ASN][1000 genomes]
rs6050710	0.94[ASN][1000 genomes]
rs6050712	0.94[ASN][1000 genomes]
rs6050714	0.94[ASN][1000 genomes]
rs6050717	0.94[ASN][1000 genomes]
rs6050720	0.94[ASN][1000 genomes]
rs6050723	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050724	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050725	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050726	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050727	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050729	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050730	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050732	0.94[ASN][1000 genomes]
rs6050733	0.94[ASN][1000 genomes]
rs6050737	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050743	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050749	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050751	0.80[ASN][1000 genomes]
rs6050753	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050754	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050755	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050756	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050757	0.84[ASN][1000 genomes]
rs6050758	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050760	0.82[ASN][1000 genomes]
rs6050763	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6050765	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050767	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050768	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050770	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050775	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050779	0.84[ASN][1000 genomes]
rs6050787	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050788	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050789	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050793	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6050795	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050796	0.86[ASN][1000 genomes]
rs6050799	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050801	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050802	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050804	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050805	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050807	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050809	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050813	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050815	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6050816	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6050825	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6050832	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050833	0.86[ASN][1000 genomes]
rs6050834	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050835	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050840	0.86[ASN][1000 genomes]
rs6050846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050853	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050858	0.80[ASN][1000 genomes]
rs6076372	0.85[ASN][1000 genomes]
rs6083886	0.82[ASN][1000 genomes]
rs6083896	0.85[ASN][1000 genomes]
rs6083897	0.85[ASN][1000 genomes]
rs6083899	0.85[ASN][1000 genomes]
rs60897995	0.86[EUR][1000 genomes]
rs61052177	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6115224	0.85[ASN][1000 genomes]
rs6138612	0.85[ASN][1000 genomes]
rs6138613	0.83[ASN][1000 genomes]
rs61494938	0.86[EUR][1000 genomes]
rs66813885	0.82[EUR][1000 genomes]
rs66983770	0.82[EUR][1000 genomes]
rs67359112	0.89[EUR][1000 genomes]
rs67455519	0.89[EUR][1000 genomes]
rs67482703	0.89[EUR][1000 genomes]
rs67921634	0.89[EUR][1000 genomes]
rs68165049	0.85[EUR][1000 genomes]
rs7261537	0.91[ASN][1000 genomes]
rs7266130	0.89[EUR][1000 genomes]
rs73339360	0.85[ASN][1000 genomes]
rs73339379	0.91[ASN][1000 genomes]
rs73339383	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73339387	0.91[ASN][1000 genomes]
rs73341305	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73341314	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73341328	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73341361	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73341363	0.97[ASN][1000 genomes]
rs73341365	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73341397	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343217	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343255	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343275	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73343292	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73345232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73345249	0.86[EUR][1000 genomes]
rs73345259	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73345264	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73345278	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73345280	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73345286	0.82[EUR][1000 genomes]
rs7346687	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73597812	0.89[EUR][1000 genomes]
rs73597813	0.89[EUR][1000 genomes]
rs73597829	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs742435	0.89[EUR][1000 genomes]
rs742436	0.89[EUR][1000 genomes]
rs8115742	0.89[EUR][1000 genomes]
rs8116267	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8116474	0.98[EUR][1000 genomes]
rs8120065	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8120594	0.94[ASN][1000 genomes]
rs8121013	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8121648	0.95[EUR][1000 genomes]
rs8122516	0.98[EUR][1000 genomes]
rs8122589	0.93[EUR][1000 genomes]
rs8125002	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8126236	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926486	0.84[ASN][1000 genomes]
rs926487	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9753575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981440	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981441	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941769	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv17092	chr20:25698651-25707971	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6050841	NINL	cis	Nerve Tibial	GTEx
rs6050841	ZNF337	cis	Stomach	GTEx
rs6050841	RP4-694B14.5	cis	Whole Blood	GTEx
rs6050841	RP4-694B14.5	cis	Stomach	GTEx
rs6050841	ZNF337	cis	lung	GTEx
rs6050841	ZNF337	cis	Adipose Subcutaneous	GTEx
rs6050841	RP4-694B14.5	cis	lung	GTEx
rs6050841	RP4-694B14.5	cis	Thyroid	GTEx
rs6050841	ZNF337	cis	Thyroid	GTEx
rs6050841	RP4-694B14.5	cis	Adipose Subcutaneous	GTEx
rs6050841	ZNF337	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25694200-25705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr20:25699400-25702600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr20:25699800-25707400	Weak transcription	Psoas Muscle	Psoas
4	chr20:25700000-25708000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr20:25700400-25701800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr20:25700400-25725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:25700600-25701600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr20:25700600-25705800	Weak transcription	Dnd41	blood
9	chr20:25701000-25701600	Weak transcription	Primary T cells from cord blood	blood
10	chr20:25701000-25701600	ZNF genes & repeats	Aorta	Aorta
11	chr20:25701000-25701600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
12	chr20:25701000-25702000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr20:25701200-25701600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr20:25701200-25702400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:25701200-25706200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr20:25701200-25706200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr20:25701200-25706200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr20:25701200-25706600	Weak transcription	Pancreas	Pancrea
19	chr20:25701200-25720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr20:25701400-25701600	Strong transcription	Brain Hippocampus Middle	brain
21	chr20:25701400-25702400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr20:25701400-25706400	Weak transcription	Esophagus	oesophagus
23	chr20:25701400-25706800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links