Variant report

Variant	rs10404574
Chromosome Location	chr19:36862082-36862083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10402405	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10414054	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10418510	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420610	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426014	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10439091	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12459465	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12971694	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12976881	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271844	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385799	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385800	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385801	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2385803	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385805	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918349	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945945	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945948	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2945949	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945950	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945951	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945957	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945961	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945963	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945971	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945972	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945992	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945993	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945994	0.90[ASN][1000 genomes]
rs2945995	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967484	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967493	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967496	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967501	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967504	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967506	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2967509	0.99[ASN][1000 genomes]
rs2967510	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967512	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967515	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967517	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967518	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967521	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967523	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967524	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967526	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2967543	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2972632	0.81[ASN][1000 genomes]
rs2972633	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4006082	0.82[ASN][1000 genomes]
rs4806321	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5021030	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58703752	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62112565	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6417185	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6510541	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6510542	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246106	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7251979	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255260	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255403	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8106095	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8109320	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109333	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112312	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10404574	LOC284412	N/A	lymphoblastoid	RTeQTL
rs10404574	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

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	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:36847400-36862200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
12	chr19:36850000-36868000	Weak transcription	Fetal Heart	heart
13	chr19:36851800-36863600	Weak transcription	Fetal Kidney	kidney
14	chr19:36852200-36867600	Weak transcription	HepG2	liver
15	chr19:36854400-36862600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr19:36855000-36862200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
17	chr19:36856600-36868400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:36857600-36865400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:36858000-36868600	Weak transcription	Brain Substantia Nigra	brain
20	chr19:36858000-36869400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:36858400-36863400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:36858400-36868200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr19:36858400-36868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:36858400-36869400	Weak transcription	Left Ventricle	heart
25	chr19:36858600-36868600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:36858600-36868600	Weak transcription	Brain Anterior Caudate	brain
27	chr19:36858600-36869200	Weak transcription	Pancreas	Pancrea
28	chr19:36858600-36869200	Weak transcription	Right Ventricle	heart
29	chr19:36858800-36868600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:36859000-36863600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:36859000-36865400	Weak transcription	Brain Angular Gyrus	brain
32	chr19:36859000-36865600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:36859000-36865800	Weak transcription	Dnd41	blood
34	chr19:36859000-36868400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:36859000-36868800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:36859000-36868800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:36859000-36869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:36859200-36865600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:36859600-36867600	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:36859800-36863600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:36860000-36862800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
42	chr19:36860800-36862200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:36860800-36862200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:36860800-36862800	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr19:36860800-36863800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
46	chr19:36861000-36862200	ZNF genes & repeats	Spleen	Spleen
47	chr19:36861000-36866000	ZNF genes & repeats	Fetal Brain Female	brain
48	chr19:36861200-36862200	ZNF genes & repeats	Brain Germinal Matrix	brain
49	chr19:36861200-36862600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr19:36861400-36862200	Active TSS	Duodenum Smooth Muscle	Duodenum

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