Variant report

Variant	rs62112631
Chromosome Location	chr19:36859987-36859988
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12461529	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462725	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17206379	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271842	1.00[AFR][1000 genomes];0.91[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	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945955	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945956	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945989	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967508	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967511	0.82[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	0.86[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];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378871	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61706074	0.82[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]
rs62112632	1.00[AFR][1000 genomes];0.86[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]
rs7253122	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73043845	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043902	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104241	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62112631	LINC00665	cis	Muscle Skeletal	GTEx
rs62112631	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs62112631	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs62112631	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs62112631	LINC00665	cis	Nerve Tibial	GTEx

Chromatin state (count:102 , 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	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
7	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
9	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:36847400-36862200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
13	chr19:36848200-36860200	Weak transcription	NHDF-Ad	bronchial
14	chr19:36848400-36861000	Weak transcription	NH-A	brain
15	chr19:36848800-36862000	Weak transcription	Hela-S3	cervix
16	chr19:36850000-36868000	Weak transcription	Fetal Heart	heart
17	chr19:36850800-36862000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr19:36851800-36863600	Weak transcription	Fetal Kidney	kidney
19	chr19:36852200-36867600	Weak transcription	HepG2	liver
20	chr19:36854400-36862000	ZNF genes & repeats	Liver	Liver
21	chr19:36854400-36862600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:36854800-36861200	Strong transcription	Brain Germinal Matrix	brain
23	chr19:36855000-36861600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
24	chr19:36855000-36862200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:36855200-36860400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:36855400-36860600	Weak transcription	HSMM	muscle
27	chr19:36855600-36860800	Weak transcription	Colonic Mucosa	Colon
28	chr19:36855600-36861200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:36856600-36868400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:36857600-36861200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:36857600-36861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:36857600-36865400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:36858000-36861400	Weak transcription	Fetal Lung	lung
34	chr19:36858000-36868600	Weak transcription	Brain Substantia Nigra	brain
35	chr19:36858000-36869400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:36858200-36860000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:36858200-36861800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
38	chr19:36858400-36861000	Weak transcription	Adipose Nuclei	Adipose
39	chr19:36858400-36861400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr19:36858400-36861600	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:36858400-36861600	Weak transcription	Fetal Brain Male	brain
42	chr19:36858400-36863400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:36858400-36868200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:36858400-36868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:36858400-36869400	Weak transcription	Left Ventricle	heart
46	chr19:36858600-36861000	Weak transcription	Spleen	Spleen
47	chr19:36858600-36861200	Weak transcription	Gastric	stomach
48	chr19:36858600-36861400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr19:36858600-36861600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:36858600-36868600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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