Variant report

Variant	rs8112156
Chromosome Location	chr19:42971608-42971609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10084159	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10401271	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10402361	0.84[AMR][1000 genomes]
rs10402677	0.94[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10403517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404402	0.81[AFR][1000 genomes]
rs10405445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405646	0.87[AMR][1000 genomes]
rs10405906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10407576	0.88[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes]
rs10411458	0.81[AFR][1000 genomes]
rs10412463	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10413413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415564	0.80[AMR][1000 genomes]
rs10416089	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10417418	0.80[AMR][1000 genomes]
rs10417693	0.80[AMR][1000 genomes]
rs10419378	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10420796	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10421108	0.86[AMR][1000 genomes]
rs10422987	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10423291	0.81[AFR][1000 genomes]
rs10469271	0.87[AMR][1000 genomes]
rs10469284	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10469286	0.88[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs1076243	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11083659	0.86[AMR][1000 genomes]
rs11665870	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11665935	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666835	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11666862	0.87[AMR][1000 genomes]
rs11668599	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671272	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671846	0.95[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11673645	0.95[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11879306	0.88[EUR][1000 genomes]
rs11881517	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11882150	0.88[EUR][1000 genomes]
rs12611218	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13343936	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16975789	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975890	0.83[EUR][1000 genomes]
rs1859341	0.80[AMR][1000 genomes]
rs2267631	0.88[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs28411988	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28447294	0.80[AMR][1000 genomes]
rs4080606	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4499340	0.80[AMR][1000 genomes]
rs55850134	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60313903	0.85[EUR][1000 genomes]
rs6509016	0.87[AFR][1000 genomes]
rs7248297	0.86[AMR][1000 genomes]
rs7253056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253209	0.86[AMR][1000 genomes]
rs8102439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102519	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8103285	0.94[ASW][hapmap];0.88[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8103891	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8106083	0.80[AMR][1000 genomes]
rs8106570	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8107152	0.88[ASW][hapmap];0.88[CEU][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8108844	0.89[YRI][hapmap]
rs851298	0.85[EUR][1000 genomes]
rs851301	0.88[EUR][1000 genomes]
rs851302	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9304604	0.82[ASW][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8112156	PTOV1	cis	parietal	SCAN
rs8112156	ZNF223	cis	parietal	SCAN
rs8112156	SEC1	cis	cerebellum	SCAN
rs8112156	KCNA7	cis	cerebellum	SCAN
rs8112156	FTL	cis	cerebellum	SCAN
rs8112156	KLK8	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr19:42965800-42972400	Enhancers	Primary B cells from peripheral blood	blood
4	chr19:42967200-42972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:42967200-42972400	Weak transcription	Esophagus	oesophagus
6	chr19:42967400-42972400	Weak transcription	Fetal Intestine Small	intestine
7	chr19:42969000-42972200	Enhancers	Primary B cells from cord blood	blood
8	chr19:42969400-42972000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr19:42969400-42973000	Enhancers	HepG2	liver
10	chr19:42969400-42975200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:42969800-42971800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr19:42970000-42971800	Enhancers	Adipose Nuclei	Adipose
13	chr19:42970000-42972600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:42970000-42972600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr19:42970000-42972600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42970000-42974600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr19:42970200-42971800	Enhancers	Brain Angular Gyrus	brain
18	chr19:42970200-42971800	Enhancers	Brain Substantia Nigra	brain
19	chr19:42970200-42972000	Enhancers	Primary hematopoietic stem cells	blood
20	chr19:42970200-42972600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:42970200-42972600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr19:42970200-42972600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr19:42970200-42972800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr19:42970200-42972800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr19:42970400-42972400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:42970400-42973000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:42970400-42973600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:42970600-42973000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:42970600-42976400	Enhancers	HSMM	muscle
30	chr19:42970800-42972400	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:42970800-42972600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:42970800-42973000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:42970800-42974600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:42970800-42974800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr19:42970800-42975000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:42970800-42975600	Weak transcription	Stomach Mucosa	stomach
37	chr19:42971000-42971800	Bivalent Enhancer	NHDF-Ad	bronchial
38	chr19:42971000-42972200	Weak transcription	Left Ventricle	heart
39	chr19:42971000-42972400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:42971000-42972400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:42971000-42972400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:42971000-42972800	Enhancers	Osteobl	bone
43	chr19:42971000-42973000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:42971000-42973400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:42971000-42973800	Weak transcription	Right Atrium	heart
46	chr19:42971000-42975400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:42971000-42975800	Weak transcription	Colonic Mucosa	Colon
48	chr19:42971000-42978000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:42971200-42972400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:42971200-42972400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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