Variant report

Variant	rs512699
Chromosome Location	chr18:44374681-44374682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10502879	0.89[CEU][hapmap]
rs10853545	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs10853547	0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs11659693	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11660085	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs1465722	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1539878	0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs1539881	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1970668	0.96[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2010834	0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs2032215	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs2156049	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2156050	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2164104	0.96[CEU][hapmap]
rs2187092	0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs2510444	0.96[ASN][1000 genomes]
rs2571028	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2576050	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2956975	0.84[AMR][1000 genomes]
rs477826	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs478820	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487386	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4890341	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap]
rs4890343	0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4890698	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4890699	0.94[JPT][hapmap]
rs4890707	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs501062	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501882	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs504668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs509647	0.87[ASN][1000 genomes]
rs513775	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs514371	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs530205	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs538221	0.96[ASN][1000 genomes]
rs541634	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs545344	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs553456	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs557089	0.96[ASN][1000 genomes]
rs557661	0.92[ASN][1000 genomes]
rs578146	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs578451	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58993513	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs590923	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs593340	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs605487	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs607780	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs612519	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs616900	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs620228	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs626217	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap]
rs629097	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs641366	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs642897	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs644731	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs646128	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs649076	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs6507709	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs658756	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs680018	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs693503	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs695001	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7227700	0.93[JPT][hapmap]
rs7240239	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs7244778	0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs8086286	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8094654	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs8095373	0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs892586	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs9304336	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304340	0.94[JPT][hapmap]
rs9916891	0.85[EUR][1000 genomes]
rs9948405	0.83[EUR][1000 genomes]
rs9954336	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs998819	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428355	chr18:44160181-44406285	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv909592	chr18:44279892-44385150	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv909593	chr18:44279892-44396246	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv909594	chr18:44279892-44400621	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv909595	chr18:44279892-44422661	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv909597	chr18:44291419-44385150	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv909598	chr18:44291419-44422661	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv909599	chr18:44294722-44385150	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv909600	chr18:44294722-44396246	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv909601	chr18:44294722-44400621	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv909602	chr18:44294722-44422661	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv909605	chr18:44316719-44422661	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv909606	chr18:44318548-44422661	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv909607	chr18:44320836-44422661	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv909608	chr18:44335724-44422661	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
17	nsv1056282	chr18:44351115-44388233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs512699	KATNAL2	cis	lymphoblastoid	seeQTL
rs512699	ST8SIA5	cis	lymphoblastoid	seeQTL
rs512699	PIAS2	cis	multi-tissue	Pritchard
rs512699	ST8SIA5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44349600-44381600	Weak transcription	Psoas Muscle	Psoas
2	chr18:44373400-44374800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:44373400-44375000	Enhancers	H9 Cell Line	embryonic stem cell
4	chr18:44373400-44375000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr18:44373400-44375400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr18:44373600-44377200	Weak transcription	Adipose Nuclei	Adipose
7	chr18:44374000-44375200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:44374200-44375200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr18:44374400-44375000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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