Variant report

Variant	rs12462271
Chromosome Location	chr19:37909470-37909471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11083427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083428	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1128327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12151218	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12151280	0.90[JPT][hapmap]
rs12162238	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12459975	0.88[EUR][1000 genomes]
rs12460230	0.90[JPT][hapmap]
rs12461941	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462524	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12986074	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12986146	0.90[JPT][hapmap]
rs17243355	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17303301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279150	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs35014847	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745764	0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3826849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv579465	chr19:37868552-37917692	ZNF genes & repeats Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv963044	chr19:37893588-37916743	ZNF genes & repeats Weak transcription Strong transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
7	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12462271	PSMC4	cis	parietal	SCAN
rs12462271	CATSPERG	cis	parietal	SCAN
rs12462271	FOSB	cis	cerebellum	SCAN
rs12462271	MRPS12	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37898000-37910000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:37898000-37910400	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37898000-37927000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:37898000-37956400	ZNF genes & repeats	Liver	Liver
5	chr19:37899200-37918800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:37900200-37927000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:37902400-37910000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:37903000-37910200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr19:37903000-37910200	ZNF genes & repeats	Dnd41	blood
10	chr19:37903200-37925000	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr19:37903200-37927200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:37903200-37936600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:37903400-37936400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
14	chr19:37905200-37913000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:37906400-37910000	ZNF genes & repeats	Brain Hippocampus Middle	brain
16	chr19:37906400-37913000	ZNF genes & repeats	Aorta	Aorta
17	chr19:37906400-37914000	ZNF genes & repeats	Left Ventricle	heart
18	chr19:37906600-37913800	ZNF genes & repeats	Ovary	ovary
19	chr19:37906600-37913800	ZNF genes & repeats	Psoas Muscle	Psoas
20	chr19:37906800-37910000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
21	chr19:37906800-37910000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:37906800-37910000	ZNF genes & repeats	Brain Substantia Nigra	brain
23	chr19:37906800-37910600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr19:37906800-37915400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr19:37906800-37918000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:37906800-37927000	ZNF genes & repeats	Fetal Brain Female	brain
27	chr19:37906800-37936600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr19:37907000-37910200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
29	chr19:37907000-37910400	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr19:37907400-37909800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:37907600-37909800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr19:37907600-37910000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
33	chr19:37907600-37910000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
34	chr19:37907600-37910000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
35	chr19:37907600-37925000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr19:37907600-37926600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
37	chr19:37907800-37909600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:37907800-37909800	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr19:37907800-37909800	ZNF genes & repeats	Right Ventricle	heart
40	chr19:37907800-37909800	ZNF genes & repeats	Small Intestine	intestine
41	chr19:37907800-37910000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:37907800-37910000	ZNF genes & repeats	Brain Anterior Caudate	brain
43	chr19:37907800-37910000	ZNF genes & repeats	A549	lung
44	chr19:37907800-37915600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr19:37907800-37926000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr19:37908000-37913800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr19:37908200-37909600	Weak transcription	Gastric	stomach
48	chr19:37908400-37910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:37908400-37911200	Weak transcription	HSMMtube	muscle
50	chr19:37908600-37909600	Weak transcription	Pancreas	Pancrea

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