Variant report

Variant	rs10919233
Chromosome Location	chr1:169732211-169732212
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL18-1	chr1:169732070-169732480	ENSG00000230704

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10489181	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489182	0.91[ASN][1000 genomes]
rs1076637	0.95[CHB][hapmap]
rs10919232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588380	0.87[EUR][1000 genomes]
rs12023614	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12027035	0.95[CHB][hapmap];0.91[MEX][hapmap]
rs12034880	0.86[ASN][1000 genomes]
rs12044082	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12072966	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12087033	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862661	0.86[EUR][1000 genomes]
rs16862663	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862672	0.90[EUR][1000 genomes]
rs2272818	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298899	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2420504	0.82[EUR][1000 genomes]
rs2420505	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs34990593	0.95[ASN][1000 genomes]
rs3917405	0.84[EUR][1000 genomes]
rs3917406	0.95[CHB][hapmap]
rs3917423	0.95[CHB][hapmap]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs4656192	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656699	0.82[EUR][1000 genomes]
rs4656700	0.82[EUR][1000 genomes]
rs4656718	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs4987301	1.00[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4987306	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4987314	1.00[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4987320	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4987322	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4987328	1.00[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs5356	1.00[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs5368	1.00[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs57793783	0.90[EUR][1000 genomes]
rs7418242	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7520701	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523319	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523520	0.89[EUR][1000 genomes]
rs7543268	0.92[ASN][1000 genomes]
rs932307	0.95[CHB][hapmap]
rs964555	1.00[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs964556	1.00[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs964557	1.00[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10919233	CNTN6	trans	lymphoblastoid	seeQTL
rs10919233	C1orf112	cis	cerebellum	SCAN
rs10919233	FMO2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169728000-169732800	Weak transcription	Adipose Nuclei	Adipose
2	chr1:169730800-169732600	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr1:169731200-169733200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:169731600-169732800	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr1:169731800-169732600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:169732200-169732400	Enhancers	Colonic Mucosa	Colon
7	chr1:169732200-169732800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:169732200-169732800	Bivalent Enhancer	Small Intestine	intestine
9	chr1:169732200-169733000	Enhancers	Fetal Intestine Large	intestine

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