Variant report

Variant	rs2306478
Chromosome Location	chr4:104003148-104003149
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	GATA3	chr4:104003137-104003281	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103996451..103999149-chr4:103999311..104004368,5	MCF-7	breast:
2	chr4:103996431..104000213-chr4:104001052..104004229,4	K562	blood:
3	chr4:104001375..104003365-chr4:104005776..104007589,2	MCF-7	breast:
4	chr4:103995898..104000159-chr4:104000809..104003700,8	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	0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.99[ASN][1000 genomes]
rs1054707	0.99[ASN][1000 genomes]
rs11724309	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs11724466	0.99[ASN][1000 genomes]
rs11724522	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11725048	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs11727029	0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs11729856	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs11730764	0.99[ASN][1000 genomes]
rs11730765	0.99[ASN][1000 genomes]
rs11734318	0.96[ASN][1000 genomes]
rs11737673	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs12500951	0.99[ASN][1000 genomes]
rs12504143	0.90[ASN][1000 genomes]
rs12504262	0.90[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505289	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12505908	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs12506065	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.99[ASN][1000 genomes]
rs12506157	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs12506198	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs12507348	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs12508269	0.88[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs12511516	0.93[ASN][1000 genomes]
rs12512468	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1381657	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1381658	0.87[CHB][hapmap];0.96[ASN][1000 genomes]
rs17215694	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs17215785	0.99[ASN][1000 genomes]
rs17215862	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17217431	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs17217592	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs17283027	0.90[ASN][1000 genomes]
rs17283077	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17283194	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17522932	0.99[ASN][1000 genomes]
rs2720469	0.87[CHD][hapmap]
rs2866633	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35714833	0.99[ASN][1000 genomes]
rs3756268	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs3756269	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs3765086	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[ASN][1000 genomes]
rs3775972	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796982	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs3796983	0.90[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];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3974474	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs55895342	0.90[ASN][1000 genomes]
rs56126326	0.99[ASN][1000 genomes]
rs56256243	0.93[ASN][1000 genomes]
rs56378042	0.90[ASN][1000 genomes]
rs56412006	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58648171	0.93[ASN][1000 genomes]
rs58888668	0.90[ASN][1000 genomes]
rs59192877	0.91[ASN][1000 genomes]
rs59341670	0.90[ASN][1000 genomes]
rs61355145	0.99[ASN][1000 genomes]
rs6533057	0.87[ASN][1000 genomes]
rs66869812	0.93[ASN][1000 genomes]
rs6822891	0.86[ASN][1000 genomes]
rs6825519	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]
rs6830791	0.99[ASN][1000 genomes]
rs6836162	0.99[ASN][1000 genomes]
rs6837114	0.91[ASN][1000 genomes]
rs6840401	0.99[ASN][1000 genomes]
rs72665040	0.99[ASN][1000 genomes]
rs72665042	0.99[ASN][1000 genomes]
rs72665048	0.99[ASN][1000 genomes]
rs72665052	0.99[ASN][1000 genomes]
rs72665054	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs72665056	0.99[ASN][1000 genomes]
rs72665063	0.96[ASN][1000 genomes]
rs72665071	0.93[ASN][1000 genomes]
rs72665093	0.90[ASN][1000 genomes]
rs72665096	0.90[ASN][1000 genomes]
rs72666812	0.91[ASN][1000 genomes]
rs736048	0.99[ASN][1000 genomes]
rs746829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs7662455	0.88[ASN][1000 genomes]
rs7664021	0.96[ASN][1000 genomes]
rs7666067	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7668568	1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7675057	0.88[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs7686105	0.96[ASN][1000 genomes]
rs7690059	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.99[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
rs2306478	BDH2	cis	cerebellum	SCAN
rs2306478	BDH2	cis	Artery Tibial	GTEx
rs2306478	PPP3CA	cis	parietal	SCAN
rs2306478	BDH2	cis	Thyroid	GTEx
rs2306478	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs2306478	BDH2	cis	lung	GTEx
rs2306478	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2306478	BDH2	cis	Esophagus Muscularis	GTEx
rs2306478	BDH2	cis	Nerve Tibial	GTEx

Chromatin state (count:115 , 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	chr4:103998200-104003200	Weak transcription	Fetal Kidney	kidney
4	chr4:103998200-104007000	Weak transcription	Lung	lung
5	chr4:103998200-104007200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:103998200-104007200	Weak transcription	Thymus	Thymus
7	chr4:103998200-104007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:103998200-104007600	Weak transcription	Gastric	stomach
9	chr4:103998200-104007800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:103998200-104008000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:103998200-104008000	Weak transcription	Placenta	Placenta
12	chr4:103998200-104010000	Weak transcription	Small Intestine	intestine
13	chr4:103998200-104011200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:103998400-104005400	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:103998400-104005400	Weak transcription	Psoas Muscle	Psoas
17	chr4:103998400-104006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:103998400-104006400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr4:103998400-104006400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:103998400-104006400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:103998400-104006800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:103998400-104006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:103998400-104007000	Weak transcription	Right Ventricle	heart
24	chr4:103998400-104007800	Weak transcription	Pancreas	Pancrea
25	chr4:103998400-104008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:103998400-104008000	Weak transcription	Colonic Mucosa	Colon
27	chr4:103998400-104008400	Weak transcription	Esophagus	oesophagus
28	chr4:103998400-104010800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:103998600-104003200	Weak transcription	HSMM	muscle
31	chr4:103998600-104005400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:103998600-104005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:103998600-104006400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:103998600-104006400	Weak transcription	GM12878-XiMat	blood
35	chr4:103998600-104006600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:103998600-104006800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:103998600-104006800	Weak transcription	Primary B cells from cord blood	blood
38	chr4:103998600-104006800	Weak transcription	NHLF	lung
39	chr4:103998600-104007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr4:103998600-104007400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:103998600-104007400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:103998600-104007600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:103998600-104007600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:103998600-104007800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:103998600-104007800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:103998600-104007800	Weak transcription	Brain Angular Gyrus	brain
47	chr4:103998600-104007800	Weak transcription	Brain Anterior Caudate	brain
48	chr4:103998600-104007800	Weak transcription	HMEC	breast
49	chr4:103998600-104007800	Weak transcription	NH-A	brain
50	chr4:103998600-104008000	Weak transcription	Brain Inferior Temporal Lobe	brain

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