Variant report

Variant	rs2504120
Chromosome Location	chr10:38394642-38394643
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1138252	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1329786	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs176876	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176877	0.80[ASN][1000 genomes]
rs176879	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176882	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176885	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176889	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008449	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2021649	0.81[ASN][1000 genomes]
rs2021650	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023299	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023351	0.80[ASN][1000 genomes]
rs2144859	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178962	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263162	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263163	0.81[ASN][1000 genomes]
rs2263164	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384731	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472173	0.80[ASN][1000 genomes]
rs2472174	0.80[ASN][1000 genomes]
rs2472175	0.81[ASN][1000 genomes]
rs2472176	0.81[ASN][1000 genomes]
rs2472177	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472178	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2472179	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2472181	0.81[ASN][1000 genomes]
rs2474554	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474563	0.80[ASN][1000 genomes]
rs2474564	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2474566	0.81[ASN][1000 genomes]
rs2474567	0.81[ASN][1000 genomes]
rs2474568	0.81[ASN][1000 genomes]
rs2474569	0.81[ASN][1000 genomes]
rs2474570	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474571	0.81[ASN][1000 genomes]
rs2474572	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2474573	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474574	0.81[ASN][1000 genomes]
rs2474575	0.81[ASN][1000 genomes]
rs2474579	0.81[ASN][1000 genomes]
rs2474580	0.81[ASN][1000 genomes]
rs2474581	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2474591	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474596	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474597	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2474610	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504121	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504127	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504139	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504140	0.81[ASN][1000 genomes]
rs2504141	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504148	0.81[ASN][1000 genomes]
rs2505179	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505185	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505186	0.81[ASN][1000 genomes]
rs2505187	0.81[ASN][1000 genomes]
rs2505188	0.81[ASN][1000 genomes]
rs2505190	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505191	0.81[ASN][1000 genomes]
rs2505193	0.81[ASN][1000 genomes]
rs2505194	0.80[ASN][1000 genomes]
rs2505195	0.80[ASN][1000 genomes]
rs2505196	0.81[ASN][1000 genomes]
rs2505197	0.81[ASN][1000 genomes]
rs2505198	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2505235	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505236	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505244	0.94[ASN][1000 genomes]
rs2505249	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505250	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2505251	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505252	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505258	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505259	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2983343	0.81[ASN][1000 genomes]
rs6482060	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7915062	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9299760	0.80[ASN][1000 genomes]
rs932538	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9418322	0.80[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2504120	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2504120	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2504120	HSD17B7P2	cis	Whole Blood	GTEx
rs2504120	HSD17B7P2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

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	chr10:38386000-38395200	Weak transcription	Hela-S3	cervix
4	chr10:38386200-38396000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr10:38386800-38395800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:38386800-38396200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr10:38386800-38396200	ZNF genes & repeats	Fetal Lung	lung
8	chr10:38387600-38398800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:38387800-38396800	ZNF genes & repeats	Liver	Liver
10	chr10:38388200-38396200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:38388200-38399200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr10:38388600-38394800	Weak transcription	NHDF-Ad	bronchial
13	chr10:38388600-38397600	Weak transcription	NH-A	brain
14	chr10:38389200-38395800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr10:38389200-38396000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
16	chr10:38389600-38395800	ZNF genes & repeats	Dnd41	blood
17	chr10:38390000-38395800	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr10:38390600-38395600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr10:38390600-38396000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr10:38390800-38395600	ZNF genes & repeats	Colon Smooth Muscle	Colon
21	chr10:38391000-38395600	ZNF genes & repeats	A549	lung
22	chr10:38391000-38396000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:38391000-38396200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:38391200-38395000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:38391200-38395600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr10:38391200-38395600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr10:38391200-38396000	ZNF genes & repeats	Fetal Kidney	kidney
28	chr10:38391200-38396400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
29	chr10:38391600-38395600	ZNF genes & repeats	Fetal Brain Male	brain
30	chr10:38391600-38395800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:38391600-38396000	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr10:38391800-38395600	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr10:38392000-38394800	Weak transcription	HepG2	liver
34	chr10:38392200-38395600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:38392200-38395600	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr10:38392400-38395600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr10:38392400-38395800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr10:38392400-38396000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:38392600-38395600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr10:38392600-38395600	ZNF genes & repeats	Fetal Stomach	stomach
41	chr10:38392600-38395800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr10:38392600-38396000	ZNF genes & repeats	Ovary	ovary
43	chr10:38392600-38396200	ZNF genes & repeats	Brain Germinal Matrix	brain
44	chr10:38392800-38395200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr10:38392800-38395600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:38392800-38395600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
47	chr10:38392800-38395600	ZNF genes & repeats	Aorta	Aorta
48	chr10:38392800-38395600	ZNF genes & repeats	Lung	lung
49	chr10:38392800-38395600	ZNF genes & repeats	Pancreas	Pancrea
50	chr10:38392800-38395600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon

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