Variant report

Variant	rs2804623
Chromosome Location	chr10:38669528-38669529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs17611180	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1892144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2145672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2505202	0.91[CHB][hapmap]
rs2505203	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2754353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2754360	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2754361	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs2754363	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2754366	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2754370	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2754493	0.80[AFR][1000 genomes]
rs2754495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs2800473	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800485	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2800551	0.95[ASN][1000 genomes]
rs2800552	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2800555	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2804622	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804624	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2804637	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2804638	0.92[ASN][1000 genomes]
rs2804639	0.87[ASN][1000 genomes]
rs2804641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804643	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804649	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs2804675	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs2804677	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3930236	0.81[AFR][1000 genomes]
rs4934948	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61837215	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6482064	0.80[AFR][1000 genomes]
rs9418368	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9730745	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	esv33710	chr10:38545898-38671289	Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv427860	chr10:38588021-38818835	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv895034	chr10:38632352-38743545	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv947859	chr10:38633447-38674546	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2764202	chr10:38641508-39076221	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1048953	chr10:38645824-39074038	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv428230	chr10:38652001-38818835	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv540567	chr10:38666856-38676001	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv540568	chr10:38666856-38684802	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2804623	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2804623	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2804623	HSD17B7P2	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38646000-38670600	Weak transcription	Fetal Stomach	stomach
2	chr10:38656400-38670000	Weak transcription	Fetal Lung	lung
3	chr10:38656600-38670600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr10:38660600-38670400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:38660600-38670600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr10:38660600-38671600	Weak transcription	HepG2	liver
7	chr10:38661000-38669800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr10:38661000-38670200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:38661000-38670200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:38661000-38670200	Weak transcription	Pancreas	Pancrea
11	chr10:38661000-38670600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:38661000-38670600	Weak transcription	Esophagus	oesophagus
13	chr10:38661000-38670800	Weak transcription	Left Ventricle	heart
14	chr10:38661000-38683400	Weak transcription	Brain Substantia Nigra	brain
15	chr10:38661200-38670400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:38661200-38670800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:38661200-38680400	Weak transcription	GM12878-XiMat	blood
18	chr10:38666800-38676000	Weak transcription	Dnd41	blood
19	chr10:38667200-38670200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:38667400-38670200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:38667400-38670600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr10:38667600-38670800	Weak transcription	Primary T cells from cord blood	blood
23	chr10:38667800-38669600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:38667800-38670600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:38668000-38669600	Weak transcription	Liver	Liver
26	chr10:38668000-38669600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:38668000-38674200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:38668200-38675000	Weak transcription	Lung	lung
29	chr10:38669200-38669600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:38669400-38669800	Weak transcription	Duodenum Mucosa	Duodenum

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