Variant report

Variant	rs2505218
Chromosome Location	chr10:38354006-38354007
allele	C/T
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];0.82[ASN][1000 genomes]
rs1208621	0.82[EUR][1000 genomes]
rs12413083	0.91[ASN][1000 genomes]
rs12414618	0.85[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];0.85[ASN][1000 genomes]
rs176831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176832	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1779073	0.84[EUR][1000 genomes]
rs2021651	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178958	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293962	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2472153	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2472159	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472160	0.99[ASN][1000 genomes]
rs2474545	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474553	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2480521	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2489166	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2504133	0.82[EUR][1000 genomes]
rs2504137	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2738221	0.84[EUR][1000 genomes]
rs664543	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs677565	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs766362	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7895468	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9418311	0.88[EUR][1000 genomes];0.87[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
rs2505218	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2505218	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2505218	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38345400-38355200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:38345600-38354400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:38346200-38358200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:38347000-38358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:38348800-38354800	Strong transcription	Primary T cells from cord blood	blood
6	chr10:38350200-38356800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr10:38350200-38358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:38350400-38354200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:38350400-38356000	Weak transcription	GM12878-XiMat	blood
10	chr10:38350600-38355000	Weak transcription	Small Intestine	intestine
11	chr10:38350600-38355200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr10:38350600-38355400	Weak transcription	Thymus	Thymus
13	chr10:38350600-38355600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:38350600-38356400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:38350600-38357800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:38350600-38358000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:38350600-38358000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:38350600-38364000	Weak transcription	Ovary	ovary
19	chr10:38351000-38355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:38351200-38354400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr10:38351200-38354800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:38351200-38355200	Weak transcription	NHEK	skin
23	chr10:38351200-38356000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:38351200-38356000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:38351200-38357800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:38351400-38354600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:38351400-38354600	Weak transcription	Placenta	Placenta
28	chr10:38351400-38354600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr10:38351600-38354400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr10:38351600-38355400	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:38352800-38355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:38353200-38354600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:38353200-38355000	Weak transcription	Dnd41	blood
34	chr10:38353200-38361400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:38353400-38355200	Weak transcription	Left Ventricle	heart
36	chr10:38353400-38355200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:38353400-38355600	Weak transcription	Primary B cells from cord blood	blood
38	chr10:38353400-38356800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:38353600-38355400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr10:38353800-38354400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:38353800-38355400	Weak transcription	Brain Germinal Matrix	brain
42	chr10:38353800-38355400	Weak transcription	Fetal Brain Female	brain
43	chr10:38354000-38355800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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