Variant report

Variant	rs1035578
Chromosome Location	chr16:12531365-12531366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1035579	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11075072	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11075073	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11643639	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11647957	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11649076	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11859542	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12051092	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12924190	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12931371	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34920830	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36011100	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4780435	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4780436	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4780437	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4780438	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4781234	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4781236	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4781237	0.87[AMR][1000 genomes]
rs4781238	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4781239	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4781240	0.87[EUR][1000 genomes]
rs62028398	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1036612	chr16:12518604-12565232	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1035578	EMP2	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12476000-12531600	Weak transcription	Right Ventricle	heart
2	chr16:12497800-12539800	Weak transcription	Left Ventricle	heart
3	chr16:12498000-12541200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:12498400-12564600	Weak transcription	Esophagus	oesophagus
5	chr16:12511400-12552000	Weak transcription	Lung	lung
6	chr16:12513200-12536600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr16:12517000-12550800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr16:12517400-12537000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:12517400-12537000	Weak transcription	Aorta	Aorta
10	chr16:12517600-12531600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:12518400-12537000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr16:12520400-12533600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:12522000-12537600	Weak transcription	Primary B cells from cord blood	blood
14	chr16:12524000-12536800	Weak transcription	Primary T cells from cord blood	blood
15	chr16:12524000-12551400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr16:12527800-12536800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:12528400-12531400	Weak transcription	Ovary	ovary
18	chr16:12528600-12532200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:12528600-12532200	Weak transcription	Thymus	Thymus
20	chr16:12528600-12533400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr16:12528600-12537800	Weak transcription	Fetal Lung	lung
22	chr16:12528800-12531400	Weak transcription	Brain Angular Gyrus	brain
23	chr16:12528800-12531600	Weak transcription	HepG2	liver
24	chr16:12528800-12564400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr16:12529000-12531600	Weak transcription	Brain Anterior Caudate	brain
26	chr16:12529800-12544400	Weak transcription	Gastric	stomach
27	chr16:12530000-12531400	Enhancers	Fetal Thymus	thymus
28	chr16:12530000-12532200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr16:12530200-12534400	Enhancers	Placenta	Placenta
30	chr16:12530400-12531400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr16:12530400-12531600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr16:12530400-12533400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:12530400-12533400	Weak transcription	Fetal Brain Female	brain
34	chr16:12530400-12533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:12530400-12533600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr16:12530400-12577600	Weak transcription	Pancreas	Pancrea
37	chr16:12530600-12533400	Weak transcription	Brain Germinal Matrix	brain
38	chr16:12531000-12531800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr16:12531000-12532000	Enhancers	Brain Hippocampus Middle	brain
40	chr16:12531000-12532200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr16:12531000-12532400	Enhancers	Fetal Muscle Leg	muscle
42	chr16:12531200-12531600	Enhancers	Spleen	Spleen
43	chr16:12531200-12531800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr16:12531200-12531800	Enhancers	GM12878-XiMat	blood
45	chr16:12531200-12532000	Enhancers	Brain Substantia Nigra	brain
46	chr16:12531200-12532600	Enhancers	Brain Cingulate Gyrus	brain
47	chr16:12531200-12534000	Enhancers	Brain Inferior Temporal Lobe	brain

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