Variant report

Variant	rs2754353
Chromosome Location	chr10:38653996-38653997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

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];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2145672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2505202	0.91[CHB][hapmap]
rs2505203	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2754360	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs2754361	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2754363	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754366	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2754370	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2754493	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2754495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs2800473	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800485	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2800551	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2800552	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2800555	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804622	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804623	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2804624	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2804631	0.80[ASN][1000 genomes]
rs2804637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2804638	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2804639	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2804641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804643	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2804649	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2804675	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs2804677	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4934948	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61837215	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6482064	0.84[AFR][1000 genomes]
rs9418368	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2754353	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2754353	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2754353	HSD17B7P2	cis	Whole Blood	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38645600-38655200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:38645600-38660000	Weak transcription	Spleen	Spleen
3	chr10:38645600-38660200	Weak transcription	Aorta	Aorta
4	chr10:38645600-38661600	Weak transcription	Small Intestine	intestine
5	chr10:38645800-38660000	Weak transcription	Esophagus	oesophagus
6	chr10:38645800-38660000	Weak transcription	Gastric	stomach
7	chr10:38645800-38660000	Weak transcription	Pancreas	Pancrea
8	chr10:38645800-38661000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:38645800-38662200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:38645800-38662400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:38645800-38669000	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:38646000-38654400	Weak transcription	Lung	lung
13	chr10:38646000-38655000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:38646000-38655000	Weak transcription	Brain Germinal Matrix	brain
15	chr10:38646000-38655000	Weak transcription	Thymus	Thymus
16	chr10:38646000-38655400	Weak transcription	Fetal Intestine Large	intestine
17	chr10:38646000-38656000	Weak transcription	Left Ventricle	heart
18	chr10:38646000-38660000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:38646000-38660000	Weak transcription	Ovary	ovary
20	chr10:38646000-38661600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr10:38646000-38661800	Weak transcription	HSMM	muscle
22	chr10:38646000-38662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:38646000-38665200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:38646000-38670600	Weak transcription	Fetal Stomach	stomach
25	chr10:38646200-38657200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:38646200-38658400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr10:38646200-38660000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr10:38646200-38660200	Weak transcription	Brain Anterior Caudate	brain
29	chr10:38646200-38662400	Weak transcription	Osteobl	bone
30	chr10:38646200-38667000	Weak transcription	Fetal Intestine Small	intestine
31	chr10:38646200-38669200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr10:38646200-38669200	Weak transcription	Right Ventricle	heart
33	chr10:38646400-38654400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr10:38646400-38654400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr10:38646400-38654400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:38646400-38654400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr10:38646400-38654800	Weak transcription	Primary B cells from cord blood	blood
38	chr10:38646400-38655200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:38646400-38656000	Weak transcription	Brain Hippocampus Middle	brain
40	chr10:38646400-38656200	Weak transcription	NHDF-Ad	bronchial
41	chr10:38646400-38660200	Weak transcription	Brain Substantia Nigra	brain
42	chr10:38646400-38660200	Weak transcription	HSMMtube	muscle
43	chr10:38646400-38661000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr10:38646400-38661000	Weak transcription	Stomach Mucosa	stomach
45	chr10:38646400-38661600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr10:38646400-38661800	Weak transcription	Brain Angular Gyrus	brain
47	chr10:38646400-38661800	Weak transcription	Fetal Kidney	kidney
48	chr10:38646400-38662200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:38646400-38662200	Weak transcription	NHLF	lung
50	chr10:38646600-38654400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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