Variant report

Variant	rs2505190
Chromosome Location	chr10:38396194-38396195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1138252	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1329786	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs176876	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176879	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs176885	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176889	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008449	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2021650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023299	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144859	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178962	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263162	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2263164	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2384731	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472177	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2472178	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2472179	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2474554	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2474564	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2474570	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474572	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2474573	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2474581	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2474591	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474596	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474597	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474610	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2504120	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504121	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504127	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504139	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504141	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505179	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505185	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505198	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2505235	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505236	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505244	0.93[ASN][1000 genomes]
rs2505249	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505250	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2505251	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505252	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505258	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505259	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6482060	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7915062	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs932538	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv550419	chr10:38311777-38501654	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv6465	chr10:38377662-38422125	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2505190	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2505190	HSD17B7P2	cis	Whole Blood	GTEx
rs2505190	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38384400-38396400	Weak transcription	HUVEC	blood vessel
2	chr10:38385600-38396200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:38386800-38396200	ZNF genes & repeats	Fetal Brain Female	brain
4	chr10:38386800-38396200	ZNF genes & repeats	Fetal Lung	lung
5	chr10:38387600-38398800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:38387800-38396800	ZNF genes & repeats	Liver	Liver
7	chr10:38388200-38396200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:38388200-38399200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr10:38388600-38397600	Weak transcription	NH-A	brain
10	chr10:38391000-38396200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:38391200-38396400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
12	chr10:38392600-38396200	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr10:38393400-38396600	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:38393600-38402400	Weak transcription	HSMMtube	muscle
15	chr10:38394400-38396200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:38394400-38396200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr10:38394600-38396200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr10:38395000-38396200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:38395000-38396200	ZNF genes & repeats	Left Ventricle	heart
20	chr10:38395200-38402400	Weak transcription	NHDF-Ad	bronchial
21	chr10:38395400-38396400	Weak transcription	Brain Angular Gyrus	brain
22	chr10:38395400-38396600	Strong transcription	Psoas Muscle	Psoas
23	chr10:38395600-38396800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr10:38395600-38397200	Weak transcription	Lung	lung
25	chr10:38395600-38397600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:38395600-38397600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:38395600-38397600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:38395600-38397800	Weak transcription	Brain Anterior Caudate	brain
29	chr10:38395600-38397800	Weak transcription	Placenta	Placenta
30	chr10:38395600-38398200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:38395600-38400600	Weak transcription	Right Ventricle	heart
32	chr10:38395600-38401000	Weak transcription	Fetal Heart	heart
33	chr10:38395600-38401800	Weak transcription	Gastric	stomach
34	chr10:38395600-38401800	Weak transcription	Pancreas	Pancrea
35	chr10:38395600-38402200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr10:38395600-38402200	Weak transcription	HepG2	liver
37	chr10:38395600-38402400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:38395600-38402400	Weak transcription	NHEK	skin
39	chr10:38395600-38403600	Weak transcription	Osteobl	bone
40	chr10:38395800-38396400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr10:38395800-38397800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:38395800-38402200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr10:38396000-38397200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:38396000-38401800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr10:38396000-38402200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr10:38396000-38402600	Weak transcription	HSMM	muscle

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