Variant report

Variant	rs55895342
Chromosome Location	chr4:104092394-104092395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10516498	0.91[ASN][1000 genomes]
rs1054707	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724309	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724466	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724522	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11725048	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11727029	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729856	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11730764	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730765	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734318	0.89[ASN][1000 genomes]
rs11737673	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500951	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504262	0.86[ASN][1000 genomes]
rs12505289	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505908	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506065	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506157	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506198	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12507348	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12508269	0.88[ASN][1000 genomes]
rs12511516	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12512468	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1381658	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17215694	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17215785	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17215862	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17217431	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17217592	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283027	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283077	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17283194	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522932	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306478	0.90[ASN][1000 genomes]
rs2866633	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35714833	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756268	0.91[ASN][1000 genomes]
rs3756269	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3765086	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775972	0.90[ASN][1000 genomes]
rs3796982	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796983	0.85[ASN][1000 genomes]
rs3974474	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56126326	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56256243	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56378042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56412006	0.86[ASN][1000 genomes]
rs58648171	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58888668	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59192877	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59341670	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61355145	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533057	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66869812	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822891	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6825519	0.86[ASN][1000 genomes]
rs6830791	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836162	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6837114	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840401	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665040	0.91[ASN][1000 genomes]
rs72665042	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665048	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665052	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665054	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665056	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665063	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665071	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665093	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665096	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666812	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736048	0.91[ASN][1000 genomes]
rs746829	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7662455	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664021	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666067	0.88[ASN][1000 genomes]
rs7668568	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675057	0.85[ASN][1000 genomes]
rs7686105	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690059	0.82[AMR][1000 genomes];0.92[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
rs55895342	BDH2	cis	Esophagus Muscularis	GTEx
rs55895342	BDH2	cis	Nerve Tibial	GTEx
rs55895342	BDH2	cis	Thyroid	GTEx
rs55895342	BDH2	cis	Artery Tibial	GTEx
rs55895342	BDH2	cis	lung	GTEx
rs55895342	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs55895342	BDH2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 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	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
3	chr4:104051000-104092600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:104065000-104113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:104073600-104118400	Weak transcription	Fetal Kidney	kidney
7	chr4:104078400-104108400	Strong transcription	Dnd41	blood
8	chr4:104080000-104101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:104086200-104092400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:104086600-104092400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:104087800-104092400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:104088600-104109000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:104089200-104092400	ZNF genes & repeats	GM12878-XiMat	blood
14	chr4:104089800-104098800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:104089800-104114800	Weak transcription	Placenta	Placenta
16	chr4:104089800-104118200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:104089800-104119000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:104090000-104092600	Weak transcription	Aorta	Aorta
19	chr4:104090000-104092600	Weak transcription	Pancreas	Pancrea
20	chr4:104090000-104097600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:104090000-104098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:104090000-104118000	Weak transcription	Fetal Stomach	stomach
23	chr4:104090000-104118600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:104090000-104119000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:104090200-104093600	Weak transcription	HUVEC	blood vessel
26	chr4:104090200-104095400	Weak transcription	HMEC	breast
27	chr4:104090200-104098400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:104090200-104098400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:104090200-104098400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:104090200-104098400	Weak transcription	Thymus	Thymus
31	chr4:104090200-104098400	Weak transcription	HepG2	liver
32	chr4:104090200-104098600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:104090200-104100000	Weak transcription	NHEK	skin
34	chr4:104090200-104100200	Weak transcription	NHLF	lung
35	chr4:104090200-104107400	Weak transcription	Primary B cells from cord blood	blood
36	chr4:104090200-104118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:104090200-104118200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:104090200-104118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:104090200-104118200	Weak transcription	Fetal Intestine Small	intestine
40	chr4:104090400-104094000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:104090400-104118200	Weak transcription	Fetal Brain Male	brain
42	chr4:104090600-104092600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr4:104090600-104107000	Weak transcription	Hela-S3	cervix
44	chr4:104090600-104109600	Weak transcription	Primary T cells from cord blood	blood
45	chr4:104090600-104117600	Weak transcription	Fetal Heart	heart
46	chr4:104090800-104094400	Weak transcription	HSMM	muscle
47	chr4:104090800-104095200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr4:104090800-104097000	Weak transcription	A549	lung
49	chr4:104090800-104097800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:104090800-104098000	Weak transcription	NH-A	brain

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