Variant report

Variant	rs6840401
Chromosome Location	chr4:104009633-104009634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103789095..103791154-chr4:104008357..104010785,2	MCF-7	breast:
2	chr4:104009215..104010720-chr4:104010992..104013903,2	K562	blood:
3	chr4:103998136..104000908-chr4:104009280..104011313,3	K562	blood:
4	chr4:104003503..104005189-chr4:104008716..104010245,2	MCF-7	breast:
5	chr4:104000908..104002877-chr4:104007976..104009657,2	K562	blood:
6	chr4:104004941..104007387-chr4:104009290..104010861,2	MCF-7	breast:
7	chr4:104005166..104007100-chr4:104007748..104010195,2	K562	blood:

Variant related genes	Relation type
ENSG00000164038	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000109332	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[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054707	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724309	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724466	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724522	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725048	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727029	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729856	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730764	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730765	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734318	0.97[ASN][1000 genomes]
rs11737673	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500951	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504143	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504262	0.94[ASN][1000 genomes]
rs12505289	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505908	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506065	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506157	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506198	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507348	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508269	0.97[ASN][1000 genomes]
rs12511516	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512468	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381658	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17215694	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215785	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215862	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217431	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17217592	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17283027	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283077	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283194	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17522932	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306478	0.99[ASN][1000 genomes]
rs2866633	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714833	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756268	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756269	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765086	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775972	0.99[ASN][1000 genomes]
rs3796982	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796983	0.93[ASN][1000 genomes]
rs3974474	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55895342	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126326	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56256243	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378042	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56412006	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58648171	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58888668	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	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533057	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66869812	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822891	0.88[ASN][1000 genomes]
rs6825519	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830791	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836162	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837114	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72665040	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665042	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665048	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665052	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665054	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665056	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665063	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665071	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665093	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665096	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72666812	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736048	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746829	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662455	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664021	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666067	0.97[ASN][1000 genomes]
rs7668568	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675057	0.93[ASN][1000 genomes]
rs7686105	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690059	0.95[AMR][1000 genomes];0.98[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
rs6840401	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs6840401	BDH2	cis	Esophagus Muscularis	GTEx
rs6840401	BDH2	cis	Thyroid	GTEx
rs6840401	BDH2	cis	Artery Tibial	GTEx
rs6840401	BDH2	cis	Muscle Skeletal	GTEx
rs6840401	BDH2	cis	Adipose Subcutaneous	GTEx
rs6840401	BDH2	cis	Nerve Tibial	GTEx
rs6840401	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs6840401	BDH2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103998200-104010000	Weak transcription	Small Intestine	intestine
2	chr4:103998200-104011200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:103998400-104010800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:103998600-104011200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:103998600-104011600	Weak transcription	NHDF-Ad	bronchial
8	chr4:103998600-104020200	Weak transcription	Fetal Brain Male	brain
9	chr4:103998800-104013400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:103998800-104019600	Weak transcription	NHEK	skin
11	chr4:103999000-104009800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:103999000-104010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:103999000-104020200	Weak transcription	Hela-S3	cervix
14	chr4:103999400-104013600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:104000000-104012400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:104000200-104016400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:104000400-104012400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr4:104000400-104014600	Strong transcription	Fetal Intestine Large	intestine
19	chr4:104000600-104016400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:104000800-104012800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:104000800-104013000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:104000800-104013600	Strong transcription	Primary T cells from cord blood	blood
23	chr4:104001000-104012400	Strong transcription	Liver	Liver
24	chr4:104001600-104013800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:104001800-104012400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:104001800-104015000	Strong transcription	Fetal Lung	lung
27	chr4:104002000-104012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:104003200-104013200	Strong transcription	HSMM	muscle
29	chr4:104003800-104011200	Weak transcription	Fetal Heart	heart
30	chr4:104005000-104013600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr4:104005000-104014000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:104005200-104013000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:104005200-104013400	Strong transcription	Adipose Nuclei	Adipose
34	chr4:104005400-104012200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:104005400-104012400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:104005400-104012400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr4:104005400-104012600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:104005400-104012600	Strong transcription	Ovary	ovary
39	chr4:104005400-104012600	Strong transcription	Dnd41	blood
40	chr4:104005400-104014800	Strong transcription	Fetal Muscle Leg	muscle
41	chr4:104005400-104015600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:104005400-104016400	Strong transcription	Fetal Thymus	thymus
43	chr4:104005600-104012400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:104005600-104012400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:104006000-104012400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:104006000-104012600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr4:104006200-104012400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr4:104006200-104012400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:104006200-104012400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:104006400-104010400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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