Variant report

Variant	rs5997838
Chromosome Location	chr22:31400018-31400019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31365415..31366956-chr22:31399078..31401450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253352	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1003480	0.86[YRI][hapmap]
rs1005252	1.00[YRI][hapmap]
rs10854601	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11089481	0.90[MEX][hapmap]
rs11089484	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12167144	0.80[AMR][1000 genomes]
rs12168307	0.80[AMR][1000 genomes]
rs1807686	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016654	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2019171	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2019182	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072132	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074578	0.83[ASW][hapmap];0.93[YRI][hapmap]
rs2079221	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2240175	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2240176	0.85[MEX][hapmap];0.84[TSI][hapmap]
rs2240177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2240179	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2240180	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2240182	0.83[ASW][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2240183	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2285918	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3747151	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3788426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804084	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3804085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3827330	0.89[MEX][hapmap];0.84[TSI][hapmap]
rs3948685	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4820916	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4820921	0.85[MEX][hapmap];0.84[TSI][hapmap]
rs4820923	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820925	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4820926	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749185	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749186	0.96[YRI][hapmap]
rs5749189	0.84[AMR][1000 genomes]
rs5749192	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5749199	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5749201	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753369	0.93[YRI][hapmap]
rs5753383	0.90[EUR][1000 genomes]
rs5753386	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5753389	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753394	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753396	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753398	1.00[YRI][hapmap]
rs5753407	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5753408	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753410	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5997802	0.90[MEX][hapmap];0.84[TSI][hapmap]
rs5997807	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5997830	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5997843	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5997846	0.96[YRI][hapmap]
rs6518726	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6518729	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs722683	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs722684	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7284767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7289831	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7290078	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7291077	0.81[AFR][1000 genomes]
rs7291199	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7291361	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs737924	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737926	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs737927	0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs739896	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8004	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8135974	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9609183	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609185	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609188	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9609193	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5997838	MORC2-AS1	cis	Nerve Tibial	GTEx
rs5997838	MORC2-AS1	cis	Thyroid	GTEx
rs5997838	C22orf27	cis	cerebellum	SCAN
rs5997838	MORC2	cis	parietal	SCAN
rs5997838	TUG1	Cis_1M	lymphoblastoid	RTeQTL
rs5997838	MORC2-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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