Variant report

Variant	rs2804677
Chromosome Location	chr10:38661569-38661570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17595383	0.80[EUR][1000 genomes]
rs17611180	0.83[ASN][1000 genomes]
rs1892144	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2145672	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2754353	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2754361	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2754363	0.88[ASN][1000 genomes]
rs2754366	0.92[ASN][1000 genomes]
rs2754370	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2754493	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2754495	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2800473	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2800551	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800552	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2800555	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2804622	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2804623	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2804624	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2804631	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2804632	0.82[EUR][1000 genomes]
rs2804637	0.96[AFR][1000 genomes]
rs2804638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2804639	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2804641	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2804643	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3932487	0.81[EUR][1000 genomes]
rs4934948	0.83[ASN][1000 genomes]
rs61837215	0.81[ASN][1000 genomes]
rs6482064	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9299772	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9418368	0.92[AFR][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
rs2804677	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2804677	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2804677	HSD17B7P2	cis	Whole Blood	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38645600-38661600	Weak transcription	Small Intestine	intestine
2	chr10:38645800-38662200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:38645800-38662400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr10:38645800-38669000	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:38646000-38661600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:38646000-38661800	Weak transcription	HSMM	muscle
7	chr10:38646000-38662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:38646000-38665200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:38646000-38670600	Weak transcription	Fetal Stomach	stomach
10	chr10:38646200-38662400	Weak transcription	Osteobl	bone
11	chr10:38646200-38667000	Weak transcription	Fetal Intestine Small	intestine
12	chr10:38646200-38669200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:38646200-38669200	Weak transcription	Right Ventricle	heart
14	chr10:38646400-38661600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:38646400-38661800	Weak transcription	Brain Angular Gyrus	brain
16	chr10:38646400-38661800	Weak transcription	Fetal Kidney	kidney
17	chr10:38646400-38662200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:38646400-38662200	Weak transcription	NHLF	lung
19	chr10:38646600-38662400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr10:38648200-38662000	Strong transcription	Liver	Liver
21	chr10:38648200-38668600	Weak transcription	HUVEC	blood vessel
22	chr10:38650400-38661600	Strong transcription	Dnd41	blood
23	chr10:38653000-38662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:38655400-38661800	Weak transcription	Brain Germinal Matrix	brain
25	chr10:38655400-38669000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:38656000-38668600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr10:38656200-38669200	Weak transcription	Primary B cells from cord blood	blood
28	chr10:38656400-38662000	Weak transcription	A549	lung
29	chr10:38656400-38662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr10:38656400-38668800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr10:38656400-38670000	Weak transcription	Fetal Lung	lung
32	chr10:38656600-38670600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:38657600-38662800	Weak transcription	HMEC	breast
34	chr10:38657600-38668600	Weak transcription	Fetal Thymus	thymus
35	chr10:38658200-38668400	Weak transcription	Placenta	Placenta
36	chr10:38658400-38662200	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:38658600-38663800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:38658800-38661600	Weak transcription	Colonic Mucosa	Colon
39	chr10:38659400-38661600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:38660200-38661800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:38660400-38662600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr10:38660400-38666000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr10:38660600-38661600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr10:38660600-38662200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:38660600-38662200	Weak transcription	Thymus	Thymus
46	chr10:38660600-38662800	Weak transcription	Gastric	stomach
47	chr10:38660600-38666600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr10:38660600-38667000	Weak transcription	Lung	lung
49	chr10:38660600-38667800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr10:38660600-38668600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links