Variant report

Variant	rs3108589
Chromosome Location	chr19:37232247-37232248
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	chr19:37230647..37232496-chr19:37235313..37237662,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10402486	0.91[ASN][1000 genomes]
rs10407386	0.81[ASN][1000 genomes]
rs10420413	0.85[GIH][hapmap]
rs11084862	0.83[ASN][1000 genomes]
rs1148393	0.82[EUR][1000 genomes]
rs11669642	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672680	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227797	0.81[CEU][hapmap]
rs1227811	0.82[EUR][1000 genomes]
rs1227812	0.82[EUR][1000 genomes]
rs1227818	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12610353	0.88[ASN][1000 genomes]
rs12982205	0.87[GIH][hapmap]
rs12986045	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12986257	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1302670	0.85[GIH][hapmap]
rs1830031	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2033077	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2245366	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2385564	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385642	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs2385643	0.80[ASN][1000 genomes]
rs3096617	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs3096618	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs3096619	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs3096622	0.80[ASN][1000 genomes]
rs3096623	0.80[ASN][1000 genomes]
rs3096627	0.80[ASN][1000 genomes]
rs3096628	0.80[ASN][1000 genomes]
rs3096629	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096630	0.82[ASN][1000 genomes]
rs3096631	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs3096632	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs3096636	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs3108166	0.91[ASN][1000 genomes]
rs3108167	0.88[ASN][1000 genomes]
rs3108168	0.85[ASN][1000 genomes]
rs3108171	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs3108172	0.89[ASN][1000 genomes]
rs3108174	0.88[ASN][1000 genomes]
rs3108179	0.88[ASN][1000 genomes]
rs3108181	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3108182	0.92[ASN][1000 genomes]
rs3108184	0.96[ASN][1000 genomes]
rs3108185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[ASN][1000 genomes]
rs3108186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[ASN][1000 genomes]
rs3108187	0.96[ASN][1000 genomes]
rs3108188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[ASN][1000 genomes]
rs3108189	0.91[ASN][1000 genomes]
rs3108190	0.83[ASN][1000 genomes]
rs3108191	0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs3108193	0.91[ASN][1000 genomes]
rs3108196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108197	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs3108205	0.93[ASN][1000 genomes]
rs3108208	0.91[ASN][1000 genomes]
rs3108209	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs3108212	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108214	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3108218	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108219	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108543	0.93[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs3108544	0.89[ASN][1000 genomes]
rs3108545	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs3108546	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs3108549	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108550	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs3108552	0.91[ASN][1000 genomes]
rs3108555	0.93[ASN][1000 genomes]
rs3108559	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.96[ASN][1000 genomes]
rs3108560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[ASN][1000 genomes]
rs3108562	0.96[ASN][1000 genomes]
rs3108563	0.94[ASN][1000 genomes]
rs3108564	0.96[ASN][1000 genomes]
rs3108565	0.99[ASN][1000 genomes]
rs3108566	0.88[ASN][1000 genomes]
rs3108568	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108570	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108572	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108573	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108574	0.88[ASN][1000 genomes]
rs3108575	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108576	0.88[ASN][1000 genomes]
rs3108577	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108579	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108580	0.93[ASW][hapmap];0.96[CHD][hapmap];0.85[YRI][hapmap]
rs3108583	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108585	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108590	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108591	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108592	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108596	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap]
rs3108597	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3108598	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap]
rs3108600	0.80[ASN][1000 genomes]
rs3108602	0.80[ASN][1000 genomes]
rs3108603	0.80[ASN][1000 genomes]
rs3108607	0.88[ASN][1000 genomes]
rs3108608	0.91[ASN][1000 genomes]
rs3108609	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.81[ASN][1000 genomes]
rs3108610	0.91[ASN][1000 genomes]
rs3111547	0.80[ASN][1000 genomes]
rs34002069	0.91[ASN][1000 genomes]
rs34395293	0.80[ASN][1000 genomes]
rs34629452	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35127048	0.86[AMR][1000 genomes]
rs35265584	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35313661	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35815897	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4092391	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4806336	0.80[ASN][1000 genomes]
rs4806350	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4806351	0.81[CEU][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58381108	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7245414	0.91[ASN][1000 genomes]
rs7248477	0.86[ASW][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs7250376	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258563	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7259256	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73037149	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8105197	0.95[ASN][1000 genomes]

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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv470139	chr19:37171201-37264190	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv911649	chr19:37203249-37257192	ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
15	esv3508979	chr19:37208161-37252433	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
16	esv3508980	chr19:37208161-37252433	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
17	esv3353886	chr19:37220161-37248967	ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3108589	LGALS4	cis	parietal	SCAN
rs3108589	PPP1R14A	cis	cerebellum	SCAN
rs3108589	CD3EAP	cis	cerebellum	SCAN
rs3108589	NFKBIB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37194000-37254000	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37194400-37253800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:37194600-37258800	ZNF genes & repeats	Liver	Liver
4	chr19:37216800-37232400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:37220200-37253800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:37220800-37235200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:37230800-37254000	ZNF genes & repeats	Left Ventricle	heart
8	chr19:37231000-37254000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:37231600-37233200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
10	chr19:37231600-37237600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle

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