Variant report

Variant	rs56256243
Chromosome Location	chr4:104070866-104070867
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	PBX3	chr4:104070849-104071353	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr4:104070789-104071380	SK-N-SH	brain:	n/a	chr4:104071158-104071166
3	GATA3	chr4:104070829-104071425	MCF-7	breast:	n/a	chr4:104071158-104071166 chr4:104071404-104071412
4	GATA3	chr4:104070783-104071449	SK-N-SH	brain:	n/a	chr4:104071158-104071166 chr4:104071404-104071412
5	TCF7L2	chr4:104070866-104071265	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:104065742..104068715-chr4:104069729..104071940,2	K562	blood:
2	chr4:104065425..104067242-chr4:104069687..104071229,2	K562	blood:
3	chr4:104061384..104063659-chr4:104069701..104071201,2	K562	blood:

Variant related genes	Relation type
CENPE	TF binding region
ENSG00000138778	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 9 )

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

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

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56256243	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs56256243	BDH2	cis	Adipose Subcutaneous	GTEx
rs56256243	BDH2	cis	Muscle Skeletal	GTEx
rs56256243	BDH2	cis	Nerve Tibial	GTEx
rs56256243	BDH2	cis	Thyroid	GTEx
rs56256243	BDH2	cis	Esophagus Muscularis	GTEx
rs56256243	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs56256243	BDH2	cis	lung	GTEx
rs56256243	BDH2	cis	Artery Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
2	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
3	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:104021400-104074600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:104029000-104089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:104029800-104089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:104030200-104089600	Weak transcription	Hela-S3	cervix
9	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
10	chr4:104039200-104077400	Strong transcription	Dnd41	blood
11	chr4:104048600-104071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:104049000-104073800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:104049000-104075200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:104049600-104078200	Weak transcription	Brain Germinal Matrix	brain
15	chr4:104049800-104074400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:104050600-104085400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:104050800-104071600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:104051000-104089200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:104051000-104092600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:104051400-104089400	Weak transcription	Placenta	Placenta
21	chr4:104051600-104088800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:104051800-104076800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:104052000-104089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:104052600-104088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:104053200-104077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:104055000-104073400	Weak transcription	Fetal Kidney	kidney
27	chr4:104055600-104089200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:104056800-104080000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:104057600-104071200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:104058800-104079400	Weak transcription	Primary T cells from cord blood	blood
32	chr4:104059200-104071800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:104059400-104087400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:104059400-104089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:104060800-104074800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:104061000-104071000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:104061000-104071200	Strong transcription	HMEC	breast
38	chr4:104061000-104071400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:104061000-104072400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:104061000-104073000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:104061400-104071600	Strong transcription	HUVEC	blood vessel
42	chr4:104061400-104075000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:104061800-104072400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:104062800-104079400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:104063800-104074800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr4:104064200-104071200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr4:104064200-104071600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:104064200-104089000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:104064600-104073400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:104065000-104071400	Weak transcription	Muscle Satellite Cultured Cells	--

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