Variant report

Variant	rs12462725
Chromosome Location	chr19:36858085-36858086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10403738	0.91[CHB][hapmap]
rs10407850	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10416509	0.91[CHB][hapmap]
rs10416742	0.91[CHB][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs10416925	0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]
rs12459704	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs12461077	0.81[CHB][hapmap]
rs12461529	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17206379	1.00[ASW][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271842	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385802	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945955	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945956	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945989	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967508	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967511	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967516	0.84[ASN][1000 genomes]
rs2967519	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098393	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3111555	0.85[ASN][1000 genomes]
rs3111556	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3810326	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	0.91[CHB][hapmap]
rs56378871	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61706074	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112567	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112568	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112569	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112624	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112631	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112632	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113869	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251745	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7253122	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73043845	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043902	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104241	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8111860	0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv174	chr19:36831719-36865415	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12462725	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs12462725	ZNF781	cis	cerebellum	SCAN
rs12462725	LINC00665	cis	Muscle Skeletal	GTEx
rs12462725	ZNF527	cis	cerebellum	SCAN
rs12462725	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs12462725	ZFP82	cis	lymphoblastoid	seeQTL
rs12462725	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs12462725	ITPKC	cis	cerebellum	SCAN
rs12462725	LINC00665	cis	Nerve Tibial	GTEx
rs12462725	ZFP14	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36827200-36862200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:36830600-36869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:36832200-36868600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:36834200-36868800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:36835800-36868800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:36836400-36858400	Weak transcription	Osteobl	bone
7	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
8	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
10	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:36845200-36858200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:36845800-36859200	Weak transcription	Fetal Thymus	thymus
14	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:36847200-36859200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:36847200-36859800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr19:36847400-36862200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
18	chr19:36848200-36860200	Weak transcription	NHDF-Ad	bronchial
19	chr19:36848400-36861000	Weak transcription	NH-A	brain
20	chr19:36848800-36862000	Weak transcription	Hela-S3	cervix
21	chr19:36850000-36868000	Weak transcription	Fetal Heart	heart
22	chr19:36850400-36859200	Strong transcription	Fetal Intestine Large	intestine
23	chr19:36850800-36862000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:36851800-36863600	Weak transcription	Fetal Kidney	kidney
25	chr19:36852200-36867600	Weak transcription	HepG2	liver
26	chr19:36854200-36858600	ZNF genes & repeats	Thymus	Thymus
27	chr19:36854200-36859800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:36854400-36858400	Strong transcription	Brain Hippocampus Middle	brain
29	chr19:36854400-36859000	ZNF genes & repeats	A549	lung
30	chr19:36854400-36859000	Strong transcription	Dnd41	blood
31	chr19:36854400-36859200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:36854400-36859600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
33	chr19:36854400-36859600	Strong transcription	Fetal Stomach	stomach
34	chr19:36854400-36862000	ZNF genes & repeats	Liver	Liver
35	chr19:36854400-36862600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
36	chr19:36854600-36858200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr19:36854600-36859000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36854600-36859000	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr19:36854600-36859200	Strong transcription	Ovary	ovary
40	chr19:36854600-36859800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:36854800-36858600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:36854800-36858800	Strong transcription	Brain Cingulate Gyrus	brain
43	chr19:36854800-36861200	Strong transcription	Brain Germinal Matrix	brain
44	chr19:36855000-36858600	Strong transcription	Brain Anterior Caudate	brain
45	chr19:36855000-36858600	Strong transcription	Right Ventricle	heart
46	chr19:36855000-36858800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:36855000-36859000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:36855000-36859000	Strong transcription	Brain Angular Gyrus	brain
49	chr19:36855000-36859000	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:36855000-36859400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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