Variant report

Variant	rs17283077
Chromosome Location	chr4:104096804-104096805
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10516498	0.89[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1054707	0.91[ASN][1000 genomes]
rs11724309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724466	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724522	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11725048	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11727029	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11730764	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730765	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734318	0.89[ASN][1000 genomes]
rs11737673	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500951	0.91[ASN][1000 genomes]
rs12504143	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504262	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs12505289	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505908	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506065	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506157	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12507348	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12508269	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12511516	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12512468	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381658	0.94[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17215694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17215785	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17215862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17217431	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17217592	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522932	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306478	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2866633	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35714833	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3756269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3765086	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775972	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3796982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3796983	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs3974474	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895342	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56126326	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56256243	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56378042	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56412006	0.86[ASN][1000 genomes]
rs58648171	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58888668	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59192877	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59341670	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61355145	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533057	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66869812	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822891	0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6825519	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs6830791	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836162	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6837114	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840401	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665040	0.91[ASN][1000 genomes]
rs72665042	0.91[ASN][1000 genomes]
rs72665048	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665052	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665054	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665056	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665063	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665071	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665093	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665096	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666812	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736048	0.91[ASN][1000 genomes]
rs746829	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7662455	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664021	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666067	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7668568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675057	0.85[ASN][1000 genomes]
rs7686105	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690059	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17283077	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs17283077	BDH2	cis	lung	GTEx
rs17283077	BDH2	cis	Nerve Tibial	GTEx
rs17283077	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs17283077	BDH2	cis	Esophagus Muscularis	GTEx
rs17283077	BDH2	cis	Thyroid	GTEx
rs17283077	BDH2	cis	Artery Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:104065000-104113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:104073600-104118400	Weak transcription	Fetal Kidney	kidney
5	chr4:104078400-104108400	Strong transcription	Dnd41	blood
6	chr4:104080000-104101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:104088600-104109000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:104089800-104098800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:104089800-104114800	Weak transcription	Placenta	Placenta
10	chr4:104089800-104118200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:104089800-104119000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:104090000-104097600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:104090000-104098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:104090000-104118000	Weak transcription	Fetal Stomach	stomach
15	chr4:104090000-104118600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:104090000-104119000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:104090200-104098400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:104090200-104098400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:104090200-104098400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:104090200-104098400	Weak transcription	Thymus	Thymus
21	chr4:104090200-104098400	Weak transcription	HepG2	liver
22	chr4:104090200-104098600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:104090200-104100000	Weak transcription	NHEK	skin
24	chr4:104090200-104100200	Weak transcription	NHLF	lung
25	chr4:104090200-104107400	Weak transcription	Primary B cells from cord blood	blood
26	chr4:104090200-104118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:104090200-104118200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:104090200-104118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:104090200-104118200	Weak transcription	Fetal Intestine Small	intestine
30	chr4:104090400-104118200	Weak transcription	Fetal Brain Male	brain
31	chr4:104090600-104107000	Weak transcription	Hela-S3	cervix
32	chr4:104090600-104109600	Weak transcription	Primary T cells from cord blood	blood
33	chr4:104090600-104117600	Weak transcription	Fetal Heart	heart
34	chr4:104090800-104097000	Weak transcription	A549	lung
35	chr4:104090800-104097800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:104090800-104098000	Weak transcription	NH-A	brain
37	chr4:104090800-104098200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:104090800-104098400	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:104090800-104098600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:104090800-104098600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:104090800-104100400	Weak transcription	Brain Germinal Matrix	brain
42	chr4:104090800-104100400	Weak transcription	Fetal Lung	lung
43	chr4:104090800-104102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:104090800-104118200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:104091000-104098800	Weak transcription	Fetal Brain Female	brain
46	chr4:104091000-104100200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:104091200-104097600	Strong transcription	NHDF-Ad	bronchial
48	chr4:104091600-104108400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:104091800-104097800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:104091800-104098400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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