Variant report

Variant	rs17206393
Chromosome Location	chr19:36938594-36938595
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11665865	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11670917	0.87[AMR][1000 genomes]
rs11672024	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11673325	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12971760	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12985198	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2385797	0.95[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2912415	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2912423	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2912435	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2912437	0.83[GIH][hapmap]
rs2912439	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2912441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945946	0.83[GIH][hapmap];0.84[TSI][hapmap]
rs2945953	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2945976	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2967443	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967444	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967445	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967446	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967449	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2967453	0.82[AMR][1000 genomes]
rs2967505	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2967528	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2967530	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967531	0.90[MEX][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967534	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967535	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967537	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967539	1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967540	1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3107235	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3107236	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3108598	0.86[CEU][hapmap];0.91[GIH][hapmap]
rs3111553	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34550124	0.87[AMR][1000 genomes]
rs34664029	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34830781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35408779	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62113910	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62113945	0.88[AMR][1000 genomes]
rs67276862	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8104181	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1067101	chr19:36901010-36956251	ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	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
5	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv1067364	chr19:36921204-36985874	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17206393	LGALS4	cis	parietal	SCAN
rs17206393	ARHGEF1	cis	cerebellum	SCAN
rs17206393	NFKBIB	cis	parietal	SCAN
rs17206393	PPP1R14A	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36931800-36946800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:36934200-36950000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:36934400-36944000	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:36934400-36946600	ZNF genes & repeats	Liver	Liver
5	chr19:36934800-36939800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr19:36935400-36938600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:36936000-36950000	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:36936200-36942600	ZNF genes & repeats	Fetal Brain Male	brain
9	chr19:36936200-36943600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:36936200-36949600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:36936400-36938600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:36936400-36943600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr19:36936400-36943600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
14	chr19:36936400-36946600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr19:36936400-36978400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:36936800-36940000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:36936800-36943800	ZNF genes & repeats	A549	lung
18	chr19:36936800-36944200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:36937200-36939600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:36937200-36943600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:36937600-36940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:36937600-36942600	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr19:36937600-36943000	ZNF genes & repeats	Psoas Muscle	Psoas
24	chr19:36937800-36943400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:36937800-36943600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
26	chr19:36937800-36944200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:36938000-36943600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
28	chr19:36938000-36943800	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr19:36938000-36946600	ZNF genes & repeats	Brain Germinal Matrix	brain
30	chr19:36938200-36938600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:36938200-36939000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr19:36938200-36939600	Weak transcription	Placenta	Placenta
33	chr19:36938200-36939800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:36938200-36939800	Weak transcription	Stomach Mucosa	stomach
35	chr19:36938200-36940000	Weak transcription	Left Ventricle	heart
36	chr19:36938200-36940000	Weak transcription	Pancreas	Pancrea
37	chr19:36938200-36940200	Weak transcription	Fetal Stomach	stomach
38	chr19:36938200-36941200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:36938200-36942600	ZNF genes & repeats	HSMM	muscle
40	chr19:36938200-36943600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
41	chr19:36938200-36943800	ZNF genes & repeats	Dnd41	blood
42	chr19:36938200-36944000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:36938200-36944200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:36938200-36946000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr19:36938200-36947200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
46	chr19:36938200-36952200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:36938400-36939800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr19:36938400-36940200	Weak transcription	Fetal Thymus	thymus
49	chr19:36938400-36942600	ZNF genes & repeats	NH-A	brain
50	chr19:36938400-36942800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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