Variant report

Variant	rs256739
Chromosome Location	chr19:37858660-37858661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1038085	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10418740	0.82[ASN][1000 genomes]
rs1236810	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs1465434	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530500	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2199644	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs256737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256742	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972596	0.86[EUR][1000 genomes]
rs320886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs45483504	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803228	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs62110388	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110389	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110390	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62110392	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62110395	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110430	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110431	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110434	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6508729	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs7251097	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs7258906	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73027379	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73027386	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7408736	0.82[ASN][1000 genomes]
rs8108650	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong 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	13 gene(s)	inside rSNPs	diseases
5	nsv1058788	chr19:37857748-37899157	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv579464	chr19:37858660-37881556	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs256739	CATSPERG	cis	parietal	SCAN
rs256739	EXOSC5	cis	cerebellum	SCAN
rs256739	IGFL4	cis	parietal	SCAN
rs256739	ITPKC	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:37854200-37861200	Weak transcription	Psoas Muscle	Psoas
3	chr19:37854200-37861400	Weak transcription	Small Intestine	intestine
4	chr19:37855000-37861400	Weak transcription	Fetal Heart	heart
5	chr19:37855000-37861600	Weak transcription	Aorta	Aorta
6	chr19:37855200-37860800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:37855200-37861000	Weak transcription	Right Ventricle	heart
8	chr19:37855200-37861200	Weak transcription	Left Ventricle	heart
9	chr19:37855200-37861400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:37855200-37861400	Weak transcription	Fetal Brain Male	brain
11	chr19:37855200-37861400	Weak transcription	NH-A	brain
12	chr19:37855400-37860400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:37855400-37860800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:37855400-37860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:37855400-37861000	Weak transcription	Fetal Kidney	kidney
16	chr19:37855400-37861400	Weak transcription	Hela-S3	cervix
17	chr19:37855600-37860600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:37855600-37860800	Weak transcription	Brain Angular Gyrus	brain
19	chr19:37855600-37861200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:37855600-37861200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:37855600-37861400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr19:37855600-37861400	Weak transcription	Ovary	ovary
23	chr19:37855600-37861400	Weak transcription	HSMMtube	muscle
24	chr19:37855600-37861400	Weak transcription	Osteobl	bone
25	chr19:37855800-37860800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:37855800-37861200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr19:37855800-37861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:37855800-37861400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:37856400-37861400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:37856400-37861400	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:37856600-37860800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:37856600-37860800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr19:37856800-37861200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:37856800-37861200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:37856800-37861200	Weak transcription	Fetal Lung	lung
36	chr19:37857000-37860400	Weak transcription	Dnd41	blood
37	chr19:37857000-37860800	Weak transcription	Adipose Nuclei	Adipose
38	chr19:37857000-37861200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:37857000-37861400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:37857200-37861200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:37857400-37860800	Weak transcription	NHDF-Ad	bronchial

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