Variant report

Variant	rs7418241
Chromosome Location	chr1:160507084-160507085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1055880	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11265424	0.83[EUR][1000 genomes]
rs11265442	0.81[CEU][hapmap]
rs11265452	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs11577695	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11583402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11585738	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590035	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12144628	0.81[CEU][hapmap]
rs12402879	0.81[CEU][hapmap]
rs12728784	0.83[CEU][hapmap]
rs1394078	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs151607	0.88[CEU][hapmap]
rs1572382	0.81[CEU][hapmap]
rs16832283	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs17381453	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17385337	0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs17385407	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs1809963	0.96[CEU][hapmap]
rs1998651	0.81[CEU][hapmap]
rs2025517	0.80[CEU][hapmap]
rs2083128	0.87[CEU][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs3733264	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733265	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733266	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs3753381	0.86[MEX][hapmap]
rs3755898	0.81[EUR][1000 genomes]
rs3766384	0.81[EUR][1000 genomes]
rs3766385	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766387	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs3766388	0.96[CEU][hapmap]
rs3766389	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs3816146	0.84[CEU][hapmap]
rs4145897	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5002947	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs56040770	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61801562	0.81[EUR][1000 genomes]
rs61801564	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61801565	0.85[EUR][1000 genomes]
rs61801567	0.85[EUR][1000 genomes]
rs61802603	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61802604	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61802605	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802606	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61802608	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61802610	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6662093	0.82[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6687641	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs6692382	0.81[CEU][hapmap]
rs6697596	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6699346	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67197441	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72708818	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72708832	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547054	0.88[CEU][hapmap]
rs7550771	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs912582	1.00[CEU][hapmap]
rs977019	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7418241	VANGL2	cis	cerebellum	SCAN
rs7418241	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs7418241	NHLH1	cis	cerebellum	SCAN
rs7418241	ADAMTS4	cis	cerebellum	SCAN
rs7418241	CD84	cis	lymphoblastoid	seeQTL
rs7418241	SLAMF6	cis	lymphoblastoid	seeQTL
rs7418241	ADAMTS4	cis	parietal	SCAN
rs7418241	ATF6	cis	parietal	SCAN
rs7418241	KCNN3	cis	cerebellum	SCAN
rs7418241	LRP1B	trans	parietal	SCAN
rs7418241	OLFML2B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160505400-160508400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:160506200-160508600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:160506200-160511400	Weak transcription	Small Intestine	intestine
4	chr1:160506600-160507200	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:160506800-160507200	Enhancers	Fetal Thymus	thymus
6	chr1:160506800-160507200	Active TSS	Stomach Mucosa	stomach
7	chr1:160506800-160507600	Active TSS	Fetal Stomach	stomach
8	chr1:160507000-160507400	Weak transcription	Thymus	Thymus
9	chr1:160507000-160507600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:160507000-160508600	Weak transcription	Rectal Mucosa Donor 31	rectum

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