Variant report

Variant	rs2720460
Chromosome Location	chr4:104054686-104054687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104053495..104055294-chr4:104059846..104061358,2	K562	blood:
2	chr4:104053175..104054720-chr4:104056287..104058753,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1031804	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12501621	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17217473	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045746	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069274	0.96[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126470	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251322	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251634	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615539	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623060	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623064	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711897	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2711898	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711899	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2720448	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720461	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720462	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720464	0.96[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720468	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720469	0.82[GIH][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720471	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2866635	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699050	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699051	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533056	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6810571	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6813563	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815783	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841136	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6850461	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	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

Variant related diseases (count:1)

Disease	PMID	Source
Testicular germ cell tumor	23666240	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2720460	PPP3CA	cis	parietal	SCAN
rs2720460	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2720460	BDH2	cis	cerebellum	SCAN
rs2720460	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs2720460	BDH2	cis	Artery Tibial	GTEx
rs2720460	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs2720460	BDH2	cis	Esophagus Muscularis	GTEx
rs2720460	BDH2	cis	Thyroid	GTEx
rs2720460	MANBA	cis	multi-tissue	Pritchard
rs2720460	BDH2	cis	lung	GTEx
rs2720460	KRT8P46	cis	lung	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021000-104056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:104021000-104058200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:104021000-104063800	Weak transcription	Fetal Stomach	stomach
4	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
5	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
6	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
7	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
8	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:104021400-104074600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:104029000-104056200	Weak transcription	Fetal Lung	lung
11	chr4:104029000-104089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:104029800-104089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:104030200-104063600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:104030200-104089600	Weak transcription	Hela-S3	cervix
15	chr4:104030800-104055800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:104031200-104069000	Weak transcription	Primary B cells from cord blood	blood
17	chr4:104031400-104057600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:104035200-104057800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
20	chr4:104039200-104058400	Weak transcription	Left Ventricle	heart
21	chr4:104039200-104077400	Strong transcription	Dnd41	blood
22	chr4:104044600-104070600	Weak transcription	HepG2	liver
23	chr4:104046200-104058400	Strong transcription	HSMM	muscle
24	chr4:104046400-104056200	Weak transcription	HMEC	breast
25	chr4:104047200-104058000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:104047200-104058200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:104047600-104058400	Weak transcription	Thymus	Thymus
28	chr4:104048600-104071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:104049000-104073800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:104049000-104075200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:104049400-104055200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:104049400-104059800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:104049400-104065600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:104049600-104078200	Weak transcription	Brain Germinal Matrix	brain
35	chr4:104049800-104056400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:104049800-104058400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:104049800-104074400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:104050200-104055200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:104050200-104057200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:104050200-104061800	Weak transcription	NHLF	lung
41	chr4:104050600-104058400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:104050600-104058800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:104050600-104085400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:104050800-104071600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:104051000-104056600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:104051000-104089200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:104051000-104092600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:104051200-104058200	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:104051400-104056200	Weak transcription	Osteobl	bone
50	chr4:104051400-104089400	Weak transcription	Placenta	Placenta

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