Variant report

Variant	rs11672440
Chromosome Location	chr19:38250958-38250959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1056405	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11083427	0.87[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11083428	0.87[CEU][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs11083430	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs11083434	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11665869	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11666021	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11666662	0.87[CEU][hapmap];0.90[JPT][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap]
rs11666738	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs11672257	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12151280	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs12162238	0.87[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12459013	0.87[CEU][hapmap];0.90[JPT][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs12460230	0.81[JPT][hapmap]
rs12460735	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12462505	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs17249047	0.89[EUR][1000 genomes]
rs2290999	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs241935	0.88[EUR][1000 genomes]
rs241952	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs241954	0.94[EUR][1000 genomes]
rs241955	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs35205379	0.87[CEU][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3848624	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4088299	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4356596	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4510143	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs60731897	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7248397	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs7254809	0.87[EUR][1000 genomes]
rs73025630	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73027418	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73035164	0.89[ASN][1000 genomes]
rs73039018	0.88[AFR][1000 genomes]
rs73041004	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73041022	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73041034	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73041045	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73041047	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs8103383	0.89[EUR][1000 genomes]

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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11672440	PLEKHG2	cis	cerebellum	SCAN
rs11672440	PSMC4	cis	parietal	SCAN
rs11672440	ZNF260,ZNF790,ZNF850P	cis	cerebellar cortex	BrainEAC

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38230800-38251400	Weak transcription	Pancreas	Pancrea
2	chr19:38230800-38252600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
4	chr19:38231000-38258200	Weak transcription	Brain Anterior Caudate	brain
5	chr19:38231000-38258400	Weak transcription	Fetal Kidney	kidney
6	chr19:38231000-38258800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:38231400-38255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:38231800-38253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:38231800-38257600	Weak transcription	HSMM	muscle
13	chr19:38231800-38258200	Weak transcription	HSMMtube	muscle
14	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
15	chr19:38232200-38253000	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:38232400-38252000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:38232400-38253600	Weak transcription	Right Ventricle	heart
18	chr19:38232400-38254000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:38232400-38255600	Weak transcription	Psoas Muscle	Psoas
20	chr19:38232400-38256600	Weak transcription	Dnd41	blood
21	chr19:38235200-38253200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:38235400-38251400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:38235400-38252800	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:38235600-38251400	Weak transcription	Fetal Muscle Leg	muscle
25	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
26	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:38237400-38252600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:38237400-38252800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:38238800-38251800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:38238800-38253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:38238800-38253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:38238800-38254000	Weak transcription	Fetal Brain Female	brain
33	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
34	chr19:38239000-38252600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:38239000-38253600	Weak transcription	Fetal Intestine Large	intestine
36	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
37	chr19:38239400-38256600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:38239400-38257400	Weak transcription	Brain Angular Gyrus	brain
39	chr19:38239600-38252600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:38242200-38258400	Weak transcription	NHDF-Ad	bronchial
41	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:38243000-38258200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:38243400-38251400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:38243400-38252800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:38243600-38251600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:38243600-38252400	Weak transcription	Primary B cells from cord blood	blood
47	chr19:38243600-38253400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:38243600-38257200	Weak transcription	Fetal Lung	lung
49	chr19:38245200-38258200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:38246200-38258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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