Variant report

Variant	rs1054707
Chromosome Location	chr4:104013796-104013797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:104012846..104015540-chr4:104018852..104022856,5	K562	blood:
2	chr4:104005677..104007990-chr4:104011266..104013978,2	K562	blood:
3	chr4:103994623..103998824-chr4:104011686..104015177,4	MCF-7	breast:
4	chr4:104009215..104010720-chr4:104010992..104013903,2	K562	blood:
5	chr4:103935447..103937592-chr4:104011447..104014383,2	K562	blood:

Variant related genes	Relation type
ENSG00000164039	Chromatin interaction
ENSG00000164038	Chromatin interaction

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

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

rs_ID	r²[population]
rs10516498	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724309	0.91[ASN][1000 genomes]
rs11724466	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724522	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725048	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727029	0.91[ASN][1000 genomes]
rs11729856	0.94[ASN][1000 genomes]
rs11730764	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730765	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734318	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737673	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500951	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504143	0.91[ASN][1000 genomes]
rs12504262	0.94[ASN][1000 genomes]
rs12505289	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505908	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506065	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506157	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506198	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507348	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508269	0.97[ASN][1000 genomes]
rs12511516	0.94[ASN][1000 genomes]
rs12512468	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381658	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17215694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215785	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215862	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217431	0.93[ASN][1000 genomes]
rs17217592	0.93[ASN][1000 genomes]
rs17283027	0.91[ASN][1000 genomes]
rs17283077	0.91[ASN][1000 genomes]
rs17283194	0.91[ASN][1000 genomes]
rs17522932	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306478	0.99[ASN][1000 genomes]
rs2866633	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714833	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756268	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765086	0.91[ASN][1000 genomes]
rs3775972	0.99[ASN][1000 genomes]
rs3796982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796983	0.93[ASN][1000 genomes]
rs3974474	0.91[ASN][1000 genomes]
rs55895342	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126326	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56256243	0.94[ASN][1000 genomes]
rs56378042	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56412006	0.94[ASN][1000 genomes]
rs58648171	0.94[ASN][1000 genomes]
rs58888668	0.91[ASN][1000 genomes]
rs59192877	0.93[ASN][1000 genomes]
rs59341670	0.91[ASN][1000 genomes]
rs61355145	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533057	0.89[ASN][1000 genomes]
rs66869812	0.94[ASN][1000 genomes]
rs6822891	0.88[ASN][1000 genomes]
rs6825519	0.94[ASN][1000 genomes]
rs6830791	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836162	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837114	0.93[ASN][1000 genomes]
rs6840401	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665040	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665042	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665048	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665052	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665054	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665056	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665063	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665071	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665093	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665096	0.91[ASN][1000 genomes]
rs72666812	0.93[ASN][1000 genomes]
rs736048	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746829	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662455	0.90[ASN][1000 genomes]
rs7664021	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666067	0.97[ASN][1000 genomes]
rs7668568	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675057	0.93[ASN][1000 genomes]
rs7686105	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690059	0.83[EUR][1000 genomes];1.00[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	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1054707	BDH2	cis	Nerve Tibial	GTEx
rs1054707	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs1054707	BDH2	cis	lung	GTEx
rs1054707	BDH2	cis	Artery Tibial	GTEx
rs1054707	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs1054707	BDH2	cis	Esophagus Muscularis	GTEx
rs1054707	BDH2	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:103998600-104020200	Weak transcription	Fetal Brain Male	brain
4	chr4:103998800-104019600	Weak transcription	NHEK	skin
5	chr4:103999000-104020200	Weak transcription	Hela-S3	cervix
6	chr4:104000200-104016400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:104000400-104014600	Strong transcription	Fetal Intestine Large	intestine
8	chr4:104000600-104016400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:104001600-104013800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:104001800-104015000	Strong transcription	Fetal Lung	lung
11	chr4:104005000-104014000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:104005400-104014800	Strong transcription	Fetal Muscle Leg	muscle
13	chr4:104005400-104015600	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:104005400-104016400	Strong transcription	Fetal Thymus	thymus
15	chr4:104006400-104014400	Strong transcription	Colon Smooth Muscle	Colon
16	chr4:104006800-104014600	Strong transcription	Fetal Kidney	kidney
17	chr4:104007000-104017800	Weak transcription	Stomach Mucosa	stomach
18	chr4:104007800-104013800	Strong transcription	NH-A	brain
19	chr4:104008000-104019400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:104008600-104015200	Weak transcription	Brain Angular Gyrus	brain
21	chr4:104009000-104020000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:104010200-104018000	Weak transcription	Colonic Mucosa	Colon
23	chr4:104010200-104019600	Weak transcription	Spleen	Spleen
24	chr4:104010600-104019200	Weak transcription	Esophagus	oesophagus
25	chr4:104011000-104016000	Weak transcription	Brain Anterior Caudate	brain
26	chr4:104011200-104019800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:104011800-104018600	Weak transcription	Small Intestine	intestine
28	chr4:104012000-104018800	Weak transcription	HSMMtube	muscle
29	chr4:104012000-104019000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:104012000-104019600	Weak transcription	HMEC	breast
31	chr4:104012200-104015000	Weak transcription	HUVEC	blood vessel
32	chr4:104012200-104016200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:104012200-104018600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:104012200-104019200	Weak transcription	Placenta	Placenta
35	chr4:104012200-104019200	Weak transcription	Psoas Muscle	Psoas
36	chr4:104012200-104019400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:104012200-104019400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:104012200-104019600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:104012200-104019800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:104012200-104019800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:104012400-104013800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:104012400-104013800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:104012400-104015000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:104012400-104016000	Weak transcription	HepG2	liver
45	chr4:104012400-104016200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:104012400-104016200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:104012400-104018000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:104012400-104018400	Weak transcription	Pancreas	Pancrea
49	chr4:104012400-104018600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:104012400-104018600	Weak transcription	Gastric	stomach

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