Variant report

Variant	rs2474553
Chromosome Location	chr10:38251000-38251001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10508861	0.82[AMR][1000 genomes]
rs1208578	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208619	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1208621	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12243792	0.80[EUR][1000 genomes]
rs12412402	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12413083	0.93[ASN][1000 genomes]
rs12414618	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1735625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17608725	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176831	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176832	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1779073	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs200907	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200909	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200913	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200941	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2021651	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178958	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293962	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472153	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472159	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2472160	0.84[ASN][1000 genomes]
rs2474542	0.86[ASN][1000 genomes]
rs2474545	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2480521	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2489166	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504137	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505218	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2738221	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2753883	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55742761	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59486180	0.81[EUR][1000 genomes]
rs766362	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895468	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9418311	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2474553	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2474553	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38238400-38253000	Weak transcription	Fetal Intestine Small	intestine
2	chr10:38239600-38264400	Weak transcription	Fetal Heart	heart
3	chr10:38239600-38264600	Weak transcription	Stomach Mucosa	stomach
4	chr10:38240800-38264000	Weak transcription	NHLF	lung
5	chr10:38241800-38264400	Weak transcription	NHEK	skin
6	chr10:38242200-38253600	Weak transcription	Esophagus	oesophagus
7	chr10:38242200-38253800	Weak transcription	Pancreas	Pancrea
8	chr10:38242400-38253400	Weak transcription	Spleen	Spleen
9	chr10:38242400-38253600	Weak transcription	Gastric	stomach
10	chr10:38242600-38264400	Weak transcription	HUVEC	blood vessel
11	chr10:38243000-38253600	Weak transcription	Right Ventricle	heart
12	chr10:38243400-38252800	Weak transcription	Dnd41	blood
13	chr10:38243400-38253800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr10:38243600-38253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr10:38243600-38256000	Weak transcription	HSMMtube	muscle
16	chr10:38244000-38253800	Weak transcription	Aorta	Aorta
17	chr10:38244200-38253400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:38244400-38253000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:38245200-38253600	Weak transcription	NH-A	brain
20	chr10:38245200-38253800	Weak transcription	Fetal Intestine Large	intestine
21	chr10:38245400-38253200	Weak transcription	Fetal Brain Male	brain
22	chr10:38245400-38253400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:38245800-38253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:38245800-38256000	Weak transcription	Osteobl	bone
25	chr10:38246000-38251000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr10:38246000-38253600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:38246000-38253600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:38246200-38253400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:38246400-38253200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:38246400-38253600	Weak transcription	Brain Substantia Nigra	brain
31	chr10:38246400-38253800	Weak transcription	HSMM	muscle
32	chr10:38246400-38257600	Weak transcription	Psoas Muscle	Psoas
33	chr10:38246400-38264000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr10:38246400-38264400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr10:38246600-38253200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:38246600-38253600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr10:38246600-38253800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:38246800-38253200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr10:38247000-38253000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr10:38247000-38253400	Weak transcription	Lung	lung
41	chr10:38247000-38253600	Weak transcription	Left Ventricle	heart
42	chr10:38247000-38263000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr10:38247200-38253200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:38247200-38253200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr10:38247200-38253800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:38247200-38253800	Weak transcription	Fetal Kidney	kidney
47	chr10:38247400-38251400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr10:38247400-38253200	Weak transcription	Brain Angular Gyrus	brain
49	chr10:38247400-38253200	Weak transcription	Brain Anterior Caudate	brain
50	chr10:38247400-38253200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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