Variant report

Variant	rs2480521
Chromosome Location	chr10:38350722-38350723
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1208578	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1208621	0.82[EUR][1000 genomes]
rs12413083	0.90[ASN][1000 genomes]
rs12414618	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1735625	0.81[EUR][1000 genomes]
rs17608725	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs176831	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs176832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1779073	0.84[EUR][1000 genomes]
rs2021651	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2178958	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293962	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472153	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2472159	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472160	0.99[ASN][1000 genomes]
rs2474545	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474553	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2489166	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2504133	0.82[EUR][1000 genomes]
rs2504137	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2505218	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738221	0.84[EUR][1000 genomes]
rs664543	0.99[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs677565	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs766362	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7895468	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9418311	0.88[EUR][1000 genomes];0.84[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	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
8	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
9	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2480521	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2480521	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL
rs2480521	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38336200-38351600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:38340800-38351200	ZNF genes & repeats	Liver	Liver
3	chr10:38340800-38351600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
4	chr10:38340800-38353400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
5	chr10:38341200-38351200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr10:38341200-38353800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:38341600-38351200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr10:38341600-38351400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr10:38341600-38351600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:38342000-38351200	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:38345400-38355200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:38345600-38353400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr10:38345600-38354400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:38345800-38353200	Strong transcription	Dnd41	blood
15	chr10:38346000-38351400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr10:38346000-38353200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr10:38346200-38351200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:38346200-38358200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr10:38346800-38351000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr10:38346800-38352400	Weak transcription	Hela-S3	cervix
21	chr10:38346800-38352600	Weak transcription	Fetal Thymus	thymus
22	chr10:38347000-38351200	Weak transcription	Stomach Mucosa	stomach
23	chr10:38347000-38351600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:38347000-38351600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr10:38347000-38358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:38347200-38352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:38347800-38351600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr10:38347800-38351600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr10:38347800-38351800	Weak transcription	HSMMtube	muscle
30	chr10:38348000-38351000	Strong transcription	Fetal Lung	lung
31	chr10:38348000-38351200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:38348000-38351400	Strong transcription	Fetal Kidney	kidney
33	chr10:38348200-38352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr10:38348200-38353400	Strong transcription	Primary B cells from cord blood	blood
35	chr10:38348600-38351200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr10:38348800-38351600	Strong transcription	Brain Hippocampus Middle	brain
37	chr10:38348800-38354800	Strong transcription	Primary T cells from cord blood	blood
38	chr10:38349000-38351200	Strong transcription	Fetal Muscle Leg	muscle
39	chr10:38349200-38350800	Strong transcription	Brain Anterior Caudate	brain
40	chr10:38349200-38351000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:38349200-38351000	ZNF genes & repeats	A549	lung
42	chr10:38349200-38351200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:38349200-38351200	ZNF genes & repeats	Esophagus	oesophagus
44	chr10:38349200-38351200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:38349200-38351200	Strong transcription	Left Ventricle	heart
46	chr10:38349200-38351200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr10:38349200-38351200	ZNF genes & repeats	Spleen	Spleen
48	chr10:38349200-38351400	ZNF genes & repeats	Aorta	Aorta
49	chr10:38349200-38351600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr10:38349200-38351600	Strong transcription	Brain Germinal Matrix	brain

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