Variant report

Variant	rs17522932
Chromosome Location	chr4:104021230-104021231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr4:104020842-104021309	GM12878	blood:	n/a	n/a
2	ZNF143	chr4:104020577-104021304	GM12878	blood:	n/a	chr4:104021030-104021045 chr4:104021034-104021052 chr4:104021041-104021050 chr4:104021043-104021052
3	CTCF	chr4:104020890-104021252	SK-N-SH_RA	brain:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
4	SIX5	chr4:104020830-104021259	A549	lung:	n/a	chr4:104021043-104021052 chr4:104021040-104021054 chr4:104021041-104021050
5	TAF1	chr4:104020857-104021305	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr4:104020973-104021255	HUVEC	blood vessel:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
7	ELF1	chr4:104020827-104021341	GM12878	blood:	n/a	n/a
8	ZNF143	chr4:104020810-104021359	Hela-S3	cervix:	n/a	chr4:104021030-104021045 chr4:104021034-104021052 chr4:104021041-104021050 chr4:104021043-104021052
9	CTCF	chr4:104021009-104021271	GM13977	blood:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
10	CTCF	chr4:104020977-104021257	MCF-7	breast:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
11	RAD21	chr4:104020776-104021363	HepG2	liver:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
12	STAT3	chr4:104020768-104021235	Hela-S3	cervix:	n/a	n/a
13	KAP1	chr4:104020517-104021543	HEK293	kidney:	n/a	n/a
14	CTCF	chr4:104021120-104021270	HFF	foreskin:	n/a	n/a
15	HCFC1	chr4:104020573-104021306	K562	blood:	n/a	n/a
16	CEBPB	chr4:104020698-104021253	A549	lung:	n/a	chr4:104020923-104020936
17	MXI1	chr4:104020851-104021297	GM12878	blood:	n/a	n/a
18	EBF1	chr4:104020816-104021243	GM12878	blood:	n/a	n/a
19	TBP	chr4:104020624-104021245	GM12878	blood:	n/a	n/a
20	ARID3A	chr4:104020866-104021330	K562	blood:	n/a	n/a
21	RAD21	chr4:104020858-104021310	GM12878	blood:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
22	CTCF	chr4:104020879-104021288	A549	lung:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
23	RAD21	chr4:104020839-104021376	GM12878	blood:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
24	CTCF	chr4:104021120-104021270	HFF-Myc	foreskin:	n/a	n/a
25	CTCF	chr4:104020954-104021263	Lung_OC	lung:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
26	TBL1XR1	chr4:104020374-104021285	K562	blood:	n/a	n/a
27	CTCF	chr4:104020984-104021237	K562	blood:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
28	POLR2A	chr4:104020719-104021260	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr4:104020897-104021264	ECC-1	luminal epithelium:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
30	JUN	chr4:104020970-104021249	H1-hESC	embryonic stem cell:	n/a	chr4:104021199-104021208
31	GTF2F1	chr4:104020757-104021232	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr4:104021100-104021250	HCM	heart:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
33	STAT3	chr4:104020826-104021302	MCF10A-Er-Src	breast:	n/a	n/a
34	YY1	chr4:104020864-104021259	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr4:104020907-104021317	HepG2	liver:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
36	RAD21	chr4:104020954-104021351	H1-hESC	embryonic stem cell:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
37	RAD21	chr4:104020924-104021334	SK-N-SH_RA	brain:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
38	CTCF	chr4:104021080-104021230	HEEpiC	esophagus:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
39	CTCF	chr4:104020802-104021402	MCF-7	breast:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
40	RAD21	chr4:104020933-104021284	K562	blood:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
41	CTCF	chr4:104021080-104021230	GM12874	blood:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
42	RAD21	chr4:104020934-104021249	GM12878	blood:	n/a	chr4:104021103-104021122 chr4:104021106-104021119 chr4:104021113-104021120
43	TEAD4	chr4:104020817-104021370	H1-hESC	embryonic stem cell:	n/a	n/a
44	CEBPB	chr4:104020771-104021250	A549	lung:	n/a	chr4:104020923-104020936
45	ELF1	chr4:104020768-104021325	MCF-7	breast:	n/a	n/a
46	CTCF	chr4:104020831-104021360	MCF-7	breast:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
47	FOS	chr4:104020889-104021367	MCF10A-Er-Src	breast:	n/a	chr4:104021199-104021208
48	BHLHE40	chr4:104020933-104021259	K562	blood:	n/a	n/a
49	CTCF	chr4:104020996-104021251	LNCaP	prostate:	n/a	chr4:104021105-104021123 chr4:104021106-104021122 chr4:104021110-104021118 chr4:104021100-104021121
50	CTCF	chr4:104021140-104021290	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:104021157..104023152-chr4:104024263..104027546,3	K562	blood:
2	chr4:103997335..103999148-chr4:104019345..104021953,2	K562	blood:
3	chr4:104021157..104023420-chr4:104024206..104027148,2	K562	blood:
4	chr4:103997337..103998985-chr4:104019484..104022200,2	K562	blood:

Variant related genes	Relation type
BDH2	TF binding region
ENSG00000164038	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10516498	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054707	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724466	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724522	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725048	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727029	0.91[ASN][1000 genomes]
rs11729856	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730764	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730765	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734318	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737673	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500951	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504143	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504262	0.94[ASN][1000 genomes]
rs12505289	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505908	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506065	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506157	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506198	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507348	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508269	0.97[ASN][1000 genomes]
rs12511516	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512468	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381658	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17215694	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215862	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217431	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17217592	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17283027	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283077	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283194	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306478	0.99[ASN][1000 genomes]
rs2866633	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714833	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756268	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756269	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765086	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775972	0.99[ASN][1000 genomes]
rs3796982	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796983	0.93[ASN][1000 genomes]
rs3974474	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55895342	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126326	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56256243	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378042	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56412006	0.94[ASN][1000 genomes]
rs58648171	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58888668	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59192877	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59341670	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61355145	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533057	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66869812	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822891	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6825519	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830791	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836162	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837114	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6840401	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665040	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665042	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665048	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665052	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665054	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665056	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665063	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665071	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665093	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665096	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72666812	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736048	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746829	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662455	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664021	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666067	0.97[ASN][1000 genomes]
rs7668568	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675057	0.93[ASN][1000 genomes]
rs7686105	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690059	0.87[AMR][1000 genomes];0.97[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17522932	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs17522932	BDH2	cis	Artery Tibial	GTEx
rs17522932	BDH2	cis	Nerve Tibial	GTEx
rs17522932	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs17522932	BDH2	cis	Esophagus Muscularis	GTEx
rs17522932	BDH2	cis	Thyroid	GTEx
rs17522932	BDH2	cis	Adipose Subcutaneous	GTEx
rs17522932	BDH2	cis	lung	GTEx
rs17522932	BDH2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104012400-104028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:104019800-104030200	Weak transcription	Esophagus	oesophagus
3	chr4:104020000-104021400	Active TSS	Stomach Smooth Muscle	stomach
4	chr4:104020000-104026400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:104020200-104021400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr4:104020400-104021800	Active TSS	HepG2	liver
7	chr4:104020800-104021400	Active TSS	Brain Cingulate Gyrus	brain
8	chr4:104020800-104022200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:104021000-104021400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:104021000-104021400	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:104021000-104021400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:104021000-104021400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:104021000-104021400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:104021000-104021400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:104021000-104021400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:104021000-104021400	Enhancers	Right Atrium	heart
17	chr4:104021000-104021400	Enhancers	Stomach Mucosa	stomach
18	chr4:104021000-104021400	Enhancers	Hela-S3	cervix
19	chr4:104021000-104021400	Enhancers	NHLF	lung
20	chr4:104021000-104026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:104021000-104026600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:104021000-104027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:104021000-104027200	Weak transcription	K562	blood
24	chr4:104021000-104028000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:104021000-104028200	Weak transcription	Brain Germinal Matrix	brain
26	chr4:104021000-104028600	Weak transcription	HSMM	muscle
27	chr4:104021000-104029800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:104021000-104031600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:104021000-104031600	Weak transcription	Placenta	Placenta
30	chr4:104021000-104033600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:104021000-104049200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:104021000-104049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:104021000-104056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr4:104021000-104058200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:104021000-104063800	Weak transcription	Fetal Stomach	stomach
36	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
37	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
38	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
39	chr4:104021200-104021400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr4:104021200-104021400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr4:104021200-104021400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:104021200-104021400	Enhancers	H9 Cell Line	embryonic stem cell
43	chr4:104021200-104021400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:104021200-104021400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:104021200-104021400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:104021200-104021400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:104021200-104021400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:104021200-104021400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr4:104021200-104021400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:104021200-104021400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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