Variant report

Variant	rs2208209
Chromosome Location	chr6:109903003-109903004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10457192	0.86[ASN][1000 genomes]
rs10457194	0.84[ASN][1000 genomes]
rs10457195	0.83[ASN][1000 genomes]
rs10499053	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782162	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10782163	0.87[ASN][1000 genomes]
rs10872034	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11153183	0.86[ASN][1000 genomes]
rs11153188	0.92[ASN][1000 genomes]
rs11153214	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11752791	0.94[ASN][1000 genomes]
rs11754340	0.94[ASN][1000 genomes]
rs11754455	0.86[ASN][1000 genomes]
rs11755641	0.95[ASN][1000 genomes]
rs12190920	0.81[EUR][1000 genomes]
rs12190996	0.81[EUR][1000 genomes]
rs12191353	0.87[ASN][1000 genomes]
rs12192776	0.91[ASN][1000 genomes]
rs12192847	0.81[EUR][1000 genomes]
rs12193719	0.95[ASN][1000 genomes]
rs12194061	0.92[ASN][1000 genomes]
rs12194157	0.91[ASN][1000 genomes]
rs12197180	0.85[ASN][1000 genomes]
rs12197838	0.84[ASN][1000 genomes]
rs12197950	0.91[ASN][1000 genomes]
rs12198938	0.86[ASN][1000 genomes]
rs12199154	0.86[ASN][1000 genomes]
rs12205140	0.82[ASN][1000 genomes]
rs12205485	0.94[ASN][1000 genomes]
rs12208018	0.94[ASN][1000 genomes]
rs12208933	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209691	0.81[EUR][1000 genomes]
rs12210706	0.84[ASN][1000 genomes]
rs12212476	0.86[ASN][1000 genomes]
rs12214639	0.95[ASN][1000 genomes]
rs12528781	0.94[ASN][1000 genomes]
rs13191066	0.94[ASN][1000 genomes]
rs13199109	0.82[ASN][1000 genomes]
rs13199135	0.95[ASN][1000 genomes]
rs13201947	0.87[ASN][1000 genomes]
rs13201951	0.89[ASN][1000 genomes]
rs13203587	0.86[ASN][1000 genomes]
rs13204102	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13204500	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1321328	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13220915	0.86[ASN][1000 genomes]
rs1406899	0.86[ASN][1000 genomes]
rs1476388	0.87[ASN][1000 genomes]
rs1960325	0.95[ASN][1000 genomes]
rs1980591	0.94[ASN][1000 genomes]
rs1998811	0.86[ASN][1000 genomes]
rs2024849	0.86[ASN][1000 genomes]
rs2024850	0.86[ASN][1000 genomes]
rs2024852	0.86[ASN][1000 genomes]
rs2024853	0.86[ASN][1000 genomes]
rs2148089	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277114	0.86[ASN][1000 genomes]
rs2357124	0.88[ASN][1000 genomes]
rs36131450	0.85[ASN][1000 genomes]
rs3807005	0.81[EUR][1000 genomes]
rs3899233	0.86[ASN][1000 genomes]
rs4490694	0.95[ASN][1000 genomes]
rs4945833	0.95[ASN][1000 genomes]
rs6568592	0.84[ASN][1000 genomes]
rs68042406	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906216	0.84[ASN][1000 genomes]
rs6911700	0.83[ASN][1000 genomes]
rs6914498	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6916579	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6920292	0.83[ASN][1000 genomes]
rs6926096	0.84[ASN][1000 genomes]
rs71541003	0.86[ASN][1000 genomes]
rs729888	0.91[ASN][1000 genomes]
rs7341297	0.84[ASN][1000 genomes]
rs749517	0.87[ASN][1000 genomes]
rs7755941	0.86[ASN][1000 genomes]
rs7767525	0.88[ASN][1000 genomes]
rs7773950	0.86[ASN][1000 genomes]
rs971434	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv917318	chr6:109885195-109982375	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2208209	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs2208209	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs2208209	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs2208209	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs2208209	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109878800-109903600	Weak transcription	Psoas Muscle	Psoas
2	chr6:109879000-109903800	Weak transcription	Thymus	Thymus
3	chr6:109879000-109906000	Weak transcription	Left Ventricle	heart
4	chr6:109879000-109917400	Weak transcription	Aorta	Aorta
5	chr6:109886000-109910600	Weak transcription	Primary B cells from cord blood	blood
6	chr6:109900800-109906000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:109903000-109903200	Strong transcription	Primary T cells from cord blood	blood

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