Variant report

Variant	rs2720469
Chromosome Location	chr4:104086484-104086485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104079778..104082068-chr4:104086350..104088852,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1031804	0.89[ASW][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516498	0.87[CHD][hapmap]
rs11724309	0.94[CHD][hapmap];0.88[GIH][hapmap]
rs11725048	0.94[CHD][hapmap];0.85[GIH][hapmap]
rs11727498	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501621	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505908	0.94[CHD][hapmap];0.88[GIH][hapmap]
rs12506065	0.94[CHD][hapmap];0.83[GIH][hapmap]
rs12508269	0.81[CHD][hapmap]
rs17215694	0.94[CHD][hapmap]
rs17215862	0.94[CHD][hapmap]
rs17217473	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17217592	0.94[CHD][hapmap];0.81[GIH][hapmap]
rs2045746	0.82[GIH][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069274	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2126470	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169508	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2251322	0.89[ASW][hapmap];0.82[GIH][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251634	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306478	0.87[CHD][hapmap]
rs2615539	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2623060	0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623064	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2623070	0.82[GIH][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2711897	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2711898	0.83[ASW][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711899	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2720448	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720458	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720460	0.82[GIH][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720461	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720462	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720464	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720468	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720471	0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866635	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3765086	0.94[CHD][hapmap];0.85[GIH][hapmap]
rs3775972	0.87[CHD][hapmap]
rs3796983	0.87[CHD][hapmap];0.80[GIH][hapmap]
rs4699050	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699051	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533056	0.89[ASW][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6810571	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813563	0.84[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815783	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822891	0.81[JPT][hapmap];0.89[YRI][hapmap]
rs6825519	0.87[CHD][hapmap];0.80[GIH][hapmap]
rs6841136	0.84[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6850461	0.89[ASW][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746829	0.87[CHD][hapmap];0.83[GIH][hapmap]
rs7656438	0.84[AMR][1000 genomes]
rs7666067	0.87[CHD][hapmap]
rs7668568	0.87[CHD][hapmap]
rs7675057	0.87[CHD][hapmap]
rs7690059	0.94[CHD][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2720469	BDH2	cis	Esophagus Muscularis	GTEx
rs2720469	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs2720469	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs2720469	BDH2	cis	Thyroid	GTEx
rs2720469	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2720469	KRT8P46	cis	lung	GTEx
rs2720469	BDH2	cis	Artery Tibial	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
2	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:104029000-104089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:104029800-104089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:104030200-104089600	Weak transcription	Hela-S3	cervix
6	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
7	chr4:104051000-104089200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:104051000-104092600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:104051400-104089400	Weak transcription	Placenta	Placenta
10	chr4:104051600-104088800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:104052000-104089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:104052600-104088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:104055600-104089200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:104059400-104087400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:104059400-104089000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:104064200-104089000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:104065000-104113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:104065600-104088800	Weak transcription	Thymus	Thymus
20	chr4:104070200-104088800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:104070400-104091200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:104071000-104089000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:104071200-104088800	Weak transcription	Fetal Intestine Large	intestine
24	chr4:104071800-104088800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:104072000-104088800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:104072200-104088800	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:104072600-104089200	Weak transcription	NHLF	lung
28	chr4:104072600-104089400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:104073600-104118400	Weak transcription	Fetal Kidney	kidney
30	chr4:104074800-104088800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:104076800-104088800	Weak transcription	Fetal Intestine Small	intestine
32	chr4:104076800-104088800	Weak transcription	Fetal Stomach	stomach
33	chr4:104076800-104092000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:104077600-104088600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:104077600-104089000	Weak transcription	Fetal Brain Female	brain
36	chr4:104077600-104089000	Weak transcription	NHDF-Ad	bronchial
37	chr4:104077800-104088800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:104077800-104089000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:104077800-104089000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:104078200-104088800	Weak transcription	HepG2	liver
41	chr4:104078400-104088800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:104078400-104089600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:104078400-104108400	Strong transcription	Dnd41	blood
44	chr4:104078800-104088800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:104078800-104088800	Weak transcription	Fetal Lung	lung
46	chr4:104078800-104088800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:104079200-104088800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:104080000-104089000	Weak transcription	Primary B cells from cord blood	blood
49	chr4:104080000-104101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:104080200-104088800	Weak transcription	Primary T cells from cord blood	blood

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