Variant report

Variant	rs12459637
Chromosome Location	chr19:37689998-37689999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10416428	0.90[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11667417	0.94[EUR][1000 genomes]
rs11673185	0.86[EUR][1000 genomes]
rs11673646	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12986074	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs1664696	0.85[JPT][hapmap]
rs172786	0.85[JPT][hapmap]
rs2385372	0.99[EUR][1000 genomes]
rs320879	0.80[JPT][hapmap]
rs320891	0.80[JPT][hapmap]
rs3745764	1.00[YRI][hapmap]
rs3826849	0.85[YRI][hapmap]
rs860386	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
2	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
3	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
4	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers 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	27 gene(s)	inside rSNPs	diseases
5	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
7	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers 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 target site	16 gene(s)	inside rSNPs	diseases
12	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12459637	SPINT2	cis	parietal	SCAN
rs12459637	AC012309.5	cis	Thyroid	GTEx
rs12459637	ZNF233	cis	parietal	SCAN
rs12459637	PSMC4	cis	parietal	SCAN
rs12459637	PSG6	cis	cerebellum	SCAN
rs12459637	CD3EAP	cis	cerebellum	SCAN
rs12459637	CATSPERG	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37673200-37690600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr19:37675000-37701000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:37679000-37700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:37680600-37700800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:37680800-37695000	Weak transcription	HSMM	muscle
6	chr19:37680800-37700800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:37680800-37700800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:37681000-37690800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:37681000-37695800	Weak transcription	NH-A	brain
10	chr19:37681000-37695800	Weak transcription	NHLF	lung
11	chr19:37681000-37700800	Weak transcription	HSMMtube	muscle
12	chr19:37681000-37700800	Weak transcription	HUVEC	blood vessel
13	chr19:37681000-37701000	Weak transcription	Fetal Heart	heart
14	chr19:37681200-37696600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:37681600-37690600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:37683200-37695200	Weak transcription	Brain Substantia Nigra	brain
17	chr19:37683400-37690000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:37683400-37697400	Weak transcription	Fetal Brain Male	brain
19	chr19:37684800-37690000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:37684800-37690200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:37685800-37690000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:37686800-37690800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:37686800-37690800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr19:37686800-37696600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:37686800-37699000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:37687000-37700800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:37687200-37690800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr19:37687400-37690000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:37687400-37690600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:37687400-37690600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr19:37687400-37692200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:37687400-37696000	Weak transcription	NHEK	skin
33	chr19:37687600-37690600	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:37687600-37690600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr19:37687600-37698400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr19:37687800-37690600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr19:37688000-37690000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr19:37688000-37690200	Strong transcription	Brain Anterior Caudate	brain
39	chr19:37688200-37690000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:37688200-37695400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:37688600-37690000	Strong transcription	Adipose Nuclei	Adipose
42	chr19:37688600-37690200	Strong transcription	Fetal Kidney	kidney
43	chr19:37688600-37690200	ZNF genes & repeats	Fetal Lung	lung
44	chr19:37688600-37690400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr19:37688600-37690400	ZNF genes & repeats	Colonic Mucosa	Colon
46	chr19:37688600-37690600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:37688600-37690600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr19:37688600-37690600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
49	chr19:37688600-37690600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:37688600-37690600	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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