Variant report

Variant	rs2474539
Chromosome Location	chr10:38327606-38327607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12413083	0.80[EUR][1000 genomes]
rs17609018	0.88[EUR][1000 genomes]
rs2247535	0.82[EUR][1000 genomes]
rs2474540	0.80[EUR][1000 genomes]
rs2504138	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2504147	0.83[EUR][1000 genomes]
rs60211584	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs664543	0.85[ASN][1000 genomes]
rs677565	0.85[ASN][1000 genomes]
rs72791791	0.82[EUR][1000 genomes]
rs72793732	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72793734	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9417290	0.84[EUR][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
rs2474539	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2474539	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL
rs2474539	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
4	chr10:38300800-38339200	Weak transcription	HSMMtube	muscle
5	chr10:38301800-38344400	Weak transcription	Hela-S3	cervix
6	chr10:38303200-38327800	Strong transcription	Primary B cells from cord blood	blood
7	chr10:38307600-38346600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:38307800-38336200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:38307800-38336600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:38307800-38343600	Weak transcription	Small Intestine	intestine
11	chr10:38307800-38344000	Weak transcription	Stomach Mucosa	stomach
12	chr10:38308000-38342200	Weak transcription	Brain Angular Gyrus	brain
13	chr10:38308600-38327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:38309000-38339200	Weak transcription	HUVEC	blood vessel
15	chr10:38309000-38342200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:38309800-38344200	Weak transcription	NH-A	brain
17	chr10:38314600-38342800	Weak transcription	Brain Substantia Nigra	brain
18	chr10:38315000-38333800	Weak transcription	Esophagus	oesophagus
19	chr10:38315000-38342800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:38316000-38339800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:38316000-38342600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:38316600-38334000	Weak transcription	K562	blood
23	chr10:38316600-38343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:38316800-38336000	Weak transcription	Colonic Mucosa	Colon
25	chr10:38316800-38339200	Weak transcription	HSMM	muscle
26	chr10:38317000-38331000	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:38318800-38339200	Weak transcription	Left Ventricle	heart
28	chr10:38319400-38327800	Strong transcription	Fetal Lung	lung
29	chr10:38319600-38331200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:38322000-38333200	Weak transcription	Pancreas	Pancrea
31	chr10:38322000-38339400	Weak transcription	Spleen	Spleen
32	chr10:38322000-38342000	Weak transcription	Gastric	stomach
33	chr10:38322000-38342600	Weak transcription	Right Ventricle	heart
34	chr10:38322400-38342800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:38323000-38330600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:38323000-38333600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr10:38323800-38342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr10:38323800-38343000	Weak transcription	Brain Hippocampus Middle	brain
39	chr10:38324000-38342000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr10:38324400-38335400	Weak transcription	NHEK	skin
41	chr10:38324600-38330600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:38324600-38331400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr10:38324600-38342000	Weak transcription	Fetal Brain Male	brain
44	chr10:38324600-38343800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr10:38325200-38329000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr10:38325200-38332600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:38325200-38333800	Weak transcription	Placenta	Placenta
48	chr10:38325200-38334000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr10:38325200-38339600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:38325200-38342000	Weak transcription	HMEC	breast

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