Variant report

Variant	rs2720458
Chromosome Location	chr4:104052963-104052964
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103939549..103942336-chr4:104052341..104054234,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164037	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1031804	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.86[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069274	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][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];0.90[JPT][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];0.90[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[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711897	1.00[CEU][hapmap];0.88[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];0.90[JPT][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	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720460	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	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720468	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720469	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720471	1.00[CEU][hapmap];0.88[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.88[CHB][hapmap];0.84[JPT][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];0.84[JPT][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];0.90[JPT][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];0.84[JPT][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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2720458	KRT8P46	cis	lung	GTEx
rs2720458	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs2720458	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs2720458	BDH2	cis	lung	GTEx
rs2720458	BDH2	cis	Thyroid	GTEx
rs2720458	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2720458	BDH2	cis	Artery Tibial	GTEx
rs2720458	BDH2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 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	chr4:104030400-104053000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:104030800-104055800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:104031200-104069000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:104031400-104053000	Weak transcription	Fetal Intestine Large	intestine
19	chr4:104031400-104057600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:104032200-104053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:104032200-104053000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:104033200-104054200	Weak transcription	NH-A	brain
23	chr4:104035200-104057800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
25	chr4:104039200-104058400	Weak transcription	Left Ventricle	heart
26	chr4:104039200-104077400	Strong transcription	Dnd41	blood
27	chr4:104041600-104053000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:104044600-104070600	Weak transcription	HepG2	liver
29	chr4:104044800-104053200	Weak transcription	K562	blood
30	chr4:104046200-104058400	Strong transcription	HSMM	muscle
31	chr4:104046400-104053200	Weak transcription	NHEK	skin
32	chr4:104046400-104056200	Weak transcription	HMEC	breast
33	chr4:104047200-104058000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:104047200-104058200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:104047600-104058400	Weak transcription	Thymus	Thymus
36	chr4:104048600-104071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:104049000-104073800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:104049000-104075200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:104049400-104055200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:104049400-104059800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:104049400-104065600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:104049600-104053200	Weak transcription	A549	lung
43	chr4:104049600-104078200	Weak transcription	Brain Germinal Matrix	brain
44	chr4:104049800-104056400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:104049800-104058400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:104049800-104074400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:104050200-104054600	Weak transcription	NHDF-Ad	bronchial
48	chr4:104050200-104055200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:104050200-104057200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:104050200-104061800	Weak transcription	NHLF	lung

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