Variant report

Variant	rs6825519
Chromosome Location	chr4:104007105-104007106
allele	C/T
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	RFX5	chr4:104006193-104007301	IMR90	lung:	n/a	n/a
2	CEBPB	chr4:104007038-104007246	HepG2	liver:	n/a	n/a
3	RFX5	chr4:104006709-104007118	K562	blood:	n/a	n/a
4	POLR2A	chr4:104007012-104007322	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr4:104006981-104007293	H1-neurons	neurons:	n/a	n/a
6	RFX5	chr4:104006588-104007210	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103997617..103999132-chr4:104006790..104008370,2	MCF-7	breast:
2	chr4:103996463..103998722-chr4:104006148..104008232,2	K562	blood:

Variant related genes	Relation type
SLC9B2	TF binding region
ENSG00000164038	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10516498	1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[ASN][1000 genomes]
rs1054707	0.94[ASN][1000 genomes]
rs11724309	0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs11724466	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11724522	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11725048	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs11727029	0.86[ASN][1000 genomes]
rs11729856	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs11730764	0.94[ASN][1000 genomes]
rs11730765	0.94[ASN][1000 genomes]
rs11734318	0.97[ASN][1000 genomes]
rs11737673	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs12500951	0.94[ASN][1000 genomes]
rs12504143	0.86[ASN][1000 genomes]
rs12504262	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505289	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505908	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs12506065	0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs12506157	0.89[CHB][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12506198	0.89[CHB][hapmap];0.94[ASN][1000 genomes]
rs12507348	0.89[CHB][hapmap];0.94[ASN][1000 genomes]
rs12508269	0.93[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12511516	0.89[ASN][1000 genomes]
rs12512468	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs1381657	0.89[CHB][hapmap]
rs1381658	0.91[ASN][1000 genomes]
rs17215694	0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[ASN][1000 genomes]
rs17215785	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17215862	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17217431	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs17217592	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.87[ASN][1000 genomes]
rs17283027	0.86[ASN][1000 genomes]
rs17283077	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs17283194	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs17522932	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306478	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720469	0.87[CHD][hapmap];0.80[GIH][hapmap]
rs2866633	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35714833	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3756268	0.89[CHB][hapmap];0.94[ASN][1000 genomes]
rs3756269	0.89[CHB][hapmap];0.94[ASN][1000 genomes]
rs3765086	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs3775972	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796982	0.88[CHB][hapmap];0.94[ASN][1000 genomes]
rs3796983	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3974474	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs55895342	0.86[ASN][1000 genomes]
rs56126326	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56256243	0.89[ASN][1000 genomes]
rs56378042	0.86[ASN][1000 genomes]
rs56412006	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58648171	0.89[ASN][1000 genomes]
rs58888668	0.86[ASN][1000 genomes]
rs59192877	0.87[ASN][1000 genomes]
rs59341670	0.86[ASN][1000 genomes]
rs61355145	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533057	0.89[ASN][1000 genomes]
rs66869812	0.89[ASN][1000 genomes]
rs6822891	0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs6830791	0.94[ASN][1000 genomes]
rs6836162	0.94[ASN][1000 genomes]
rs6837114	0.87[ASN][1000 genomes]
rs6840401	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665040	0.94[ASN][1000 genomes]
rs72665042	0.94[ASN][1000 genomes]
rs72665048	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665052	0.94[ASN][1000 genomes]
rs72665054	0.94[ASN][1000 genomes]
rs72665056	0.94[ASN][1000 genomes]
rs72665063	0.91[ASN][1000 genomes]
rs72665071	0.89[ASN][1000 genomes]
rs72665093	0.86[ASN][1000 genomes]
rs72665096	0.86[ASN][1000 genomes]
rs72666812	0.87[ASN][1000 genomes]
rs736048	0.94[ASN][1000 genomes]
rs746829	0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7662455	0.84[ASN][1000 genomes]
rs7664021	0.91[ASN][1000 genomes]
rs7666067	0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs7668568	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7675057	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7686105	0.91[ASN][1000 genomes]
rs7690059	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.94[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
rs6825519	BDH2	cis	Adipose Subcutaneous	GTEx
rs6825519	BDH2	cis	Thyroid	GTEx
rs6825519	PPP3CA	cis	parietal	SCAN
rs6825519	BDH2	cis	Nerve Tibial	GTEx
rs6825519	BDH2	cis	cerebellum	SCAN
rs6825519	BDH2	cis	Artery Tibial	GTEx
rs6825519	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs6825519	BDH2	cis	lung	GTEx
rs6825519	BDH2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103997800-104007800	Weak transcription	Spleen	Spleen
2	chr4:103998000-104007600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:103998200-104007200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:103998200-104007200	Weak transcription	Thymus	Thymus
5	chr4:103998200-104007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:103998200-104007600	Weak transcription	Gastric	stomach
7	chr4:103998200-104007800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:103998200-104008000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:103998200-104008000	Weak transcription	Placenta	Placenta
10	chr4:103998200-104010000	Weak transcription	Small Intestine	intestine
11	chr4:103998200-104011200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:103998400-104007800	Weak transcription	Pancreas	Pancrea
14	chr4:103998400-104008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:103998400-104008000	Weak transcription	Colonic Mucosa	Colon
16	chr4:103998400-104008400	Weak transcription	Esophagus	oesophagus
17	chr4:103998400-104010800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:103998600-104007400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:103998600-104007400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:103998600-104007600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:103998600-104007600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:103998600-104007800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:103998600-104007800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:103998600-104007800	Weak transcription	Brain Angular Gyrus	brain
26	chr4:103998600-104007800	Weak transcription	Brain Anterior Caudate	brain
27	chr4:103998600-104007800	Weak transcription	HMEC	breast
28	chr4:103998600-104007800	Weak transcription	NH-A	brain
29	chr4:103998600-104008000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:103998600-104009600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:103998600-104011200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:103998600-104011600	Weak transcription	NHDF-Ad	bronchial
33	chr4:103998600-104020200	Weak transcription	Fetal Brain Male	brain
34	chr4:103998800-104007600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:103998800-104009600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:103998800-104013400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:103998800-104019600	Weak transcription	NHEK	skin
38	chr4:103999000-104007800	Weak transcription	HepG2	liver
39	chr4:103999000-104009800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:103999000-104010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:103999000-104020200	Weak transcription	Hela-S3	cervix
42	chr4:103999400-104013600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:104000000-104012400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:104000200-104016400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:104000400-104012400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr4:104000400-104014600	Strong transcription	Fetal Intestine Large	intestine
47	chr4:104000600-104016400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:104000800-104012800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:104000800-104013000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:104000800-104013600	Strong transcription	Primary T cells from cord blood	blood

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