Variant report

Variant	rs6510542
Chromosome Location	chr19:36893856-36893857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10402405	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10404574	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10414054	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10418510	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420610	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426014	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10439091	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12459465	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12971694	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12976881	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271844	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385800	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2385801	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2385803	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385805	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918349	0.83[ASN][1000 genomes]
rs2945945	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945948	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2945949	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945950	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945951	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945957	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945961	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945963	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945971	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945972	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945992	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945993	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2945994	0.87[ASN][1000 genomes]
rs2945995	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967484	0.83[ASN][1000 genomes]
rs2967501	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967504	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967506	0.92[ASN][1000 genomes]
rs2967509	0.93[ASN][1000 genomes]
rs2967510	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967512	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967515	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967517	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967518	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967521	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967523	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967524	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967526	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2967543	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2972633	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5021030	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58703752	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112565	0.80[ASN][1000 genomes]
rs6417185	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6510541	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7246106	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7251979	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255260	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255403	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106095	0.92[ASN][1000 genomes]
rs8109320	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109333	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112312	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182628	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6510542	LOC284412	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36880400-36904600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36882400-36896600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:36882600-36904200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:36883000-36905200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:36885600-36908000	Weak transcription	K562	blood
8	chr19:36886400-36901000	Weak transcription	Stomach Mucosa	stomach
9	chr19:36886600-36895200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:36886600-36895200	Weak transcription	Right Ventricle	heart
11	chr19:36886600-36898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:36886800-36895000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:36888400-36901200	Strong transcription	Brain Hippocampus Middle	brain
14	chr19:36888800-36895000	Weak transcription	Fetal Thymus	thymus
15	chr19:36889600-36900200	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr19:36889800-36908200	Weak transcription	HepG2	liver
17	chr19:36890400-36895000	Weak transcription	Colonic Mucosa	Colon
18	chr19:36890400-36901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:36890600-36895000	Weak transcription	Pancreas	Pancrea
20	chr19:36891000-36896600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:36891000-36904800	Strong transcription	Dnd41	blood
22	chr19:36891200-36898000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:36891200-36901400	ZNF genes & repeats	A549	lung
24	chr19:36891400-36895000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:36891400-36900200	Strong transcription	Fetal Muscle Leg	muscle
26	chr19:36891600-36895000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:36891600-36895000	Weak transcription	HSMM	muscle
28	chr19:36891800-36894800	Weak transcription	Brain Substantia Nigra	brain
29	chr19:36891800-36894800	Weak transcription	NHLF	lung
30	chr19:36891800-36895400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:36891800-36898800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:36891800-36908200	Weak transcription	Fetal Heart	heart
33	chr19:36891800-36908200	Weak transcription	Hela-S3	cervix
34	chr19:36892200-36895000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:36892400-36894400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:36892400-36895000	Weak transcription	Spleen	Spleen
37	chr19:36892400-36898600	Weak transcription	NHEK	skin
38	chr19:36892400-36899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:36892400-36901400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:36892400-36901600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:36892600-36894400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:36892600-36895000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:36892600-36895200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:36892600-36896200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr19:36892800-36894000	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:36892800-36894400	Weak transcription	Fetal Brain Female	brain
47	chr19:36892800-36894800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:36892800-36894800	Weak transcription	HSMMtube	muscle
49	chr19:36892800-36895000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:36892800-36895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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