Variant report

Variant	rs61706074
Chromosome Location	chr19:36854795-36854796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

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	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17206379	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271842	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385802	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945955	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945956	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945989	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967508	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967516	0.84[ASN][1000 genomes]
rs2967519	0.82[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	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378871	0.81[EUR][1000 genomes];0.95[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	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112632	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113869	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253122	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73043845	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043902	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104241	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv579459	chr19:36845537-36856379	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs61706074	LINC00665	cis	Nerve Tibial	GTEx
rs61706074	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs61706074	LINC00665	cis	Artery Aorta	GTEx
rs61706074	LINC00665	cis	Muscle Skeletal	GTEx
rs61706074	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs61706074	LINC00665	cis	Adipose Subcutaneous	GTEx
rs61706074	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs61706074	CTD-3162L10.1	cis	Nerve Tibial	GTEx

Chromatin state (count:111 , 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	chr19:36834000-36857400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:36834200-36868800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:36835800-36857200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:36835800-36868800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:36836400-36858400	Weak transcription	Osteobl	bone
9	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
10	chr19:36836600-36857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
13	chr19:36838200-36855000	Weak transcription	HSMM	muscle
14	chr19:36840000-36855000	Weak transcription	Right Ventricle	heart
15	chr19:36840000-36856000	Weak transcription	Fetal Lung	lung
16	chr19:36841200-36854800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:36845200-36858200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:36845800-36859200	Weak transcription	Fetal Thymus	thymus
21	chr19:36846000-36855000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:36847200-36859200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr19:36847200-36859800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr19:36847400-36862200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
26	chr19:36847600-36855800	Weak transcription	Fetal Muscle Leg	muscle
27	chr19:36848200-36860200	Weak transcription	NHDF-Ad	bronchial
28	chr19:36848400-36861000	Weak transcription	NH-A	brain
29	chr19:36848800-36862000	Weak transcription	Hela-S3	cervix
30	chr19:36850000-36854800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:36850000-36855000	Weak transcription	Colonic Mucosa	Colon
32	chr19:36850000-36857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:36850000-36868000	Weak transcription	Fetal Heart	heart
34	chr19:36850200-36855000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr19:36850400-36859200	Strong transcription	Fetal Intestine Large	intestine
36	chr19:36850800-36862000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr19:36851400-36855000	Weak transcription	Esophagus	oesophagus
38	chr19:36851400-36855000	Weak transcription	Pancreas	Pancrea
39	chr19:36851400-36857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:36851600-36856000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:36851800-36855000	Weak transcription	Left Ventricle	heart
42	chr19:36851800-36855000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:36851800-36856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:36851800-36857200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:36851800-36857400	Weak transcription	HSMMtube	muscle
46	chr19:36851800-36863600	Weak transcription	Fetal Kidney	kidney
47	chr19:36852200-36867600	Weak transcription	HepG2	liver
48	chr19:36852400-36856000	Weak transcription	Fetal Intestine Small	intestine
49	chr19:36852800-36856400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr19:36853000-36855000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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