Variant report

Variant	rs3760848
Chromosome Location	chr19:56981382-56981383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10404523	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410530	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10413986	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423274	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462739	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs4801321	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs4801322	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs60732696	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66718632	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258501	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs8112950	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active 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	88 gene(s)	inside rSNPs	diseases
7	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3760848	ZNF667	cis	Nerve Tibial	GTEx
rs3760848	ZNF552	cis	parietal	SCAN
rs3760848	ZNF548	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56957200-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:56967200-56987600	Weak transcription	Fetal Heart	heart
6	chr19:56969400-56987600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:56970200-56981400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:56972800-56987600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:56973000-56981400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:56973000-56981600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:56973400-56981600	Weak transcription	Psoas Muscle	Psoas
12	chr19:56973400-56983600	Weak transcription	Dnd41	blood
13	chr19:56973600-56981800	Weak transcription	Left Ventricle	heart
14	chr19:56974000-56981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:56974000-56981600	Weak transcription	Right Ventricle	heart
16	chr19:56975600-56985200	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:56975600-56987200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:56976800-56987200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:56977400-56981400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:56978000-56984400	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr19:56978600-56981400	Weak transcription	HSMMtube	muscle
22	chr19:56979400-56982600	ZNF genes & repeats	Fetal Brain Male	brain
23	chr19:56979800-56981400	Weak transcription	Brain Angular Gyrus	brain
24	chr19:56979800-56981800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
25	chr19:56979800-56985000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
26	chr19:56980000-56982400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:56980000-56986000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr19:56980200-56981400	Weak transcription	Fetal Kidney	kidney
29	chr19:56980200-56984000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr19:56980200-56984000	ZNF genes & repeats	Fetal Stomach	stomach
31	chr19:56980200-56985000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
32	chr19:56980400-56982200	ZNF genes & repeats	Brain Hippocampus Middle	brain
33	chr19:56980400-56982200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
34	chr19:56980400-56982200	ZNF genes & repeats	Spleen	Spleen
35	chr19:56980400-56983800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:56980400-56984000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:56980400-56985800	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr19:56980400-56987200	ZNF genes & repeats	Fetal Brain Female	brain
39	chr19:56981000-56982200	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr19:56981000-56982400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:56981000-56982600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:56981000-56982600	ZNF genes & repeats	Pancreas	Pancrea
43	chr19:56981000-56984000	Strong transcription	Brain Anterior Caudate	brain
44	chr19:56981000-56984200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr19:56981000-56984800	ZNF genes & repeats	Fetal Intestine Large	intestine
46	chr19:56981000-56987600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr19:56981000-56988000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr19:56981200-56981600	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr19:56981200-56982400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:56981200-56983400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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