Variant report

Variant	rs28660600
Chromosome Location	chr3:121482637-121482638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121480892..121483629-chr3:121486983..121489016,2	K562	blood:
2	chr3:121468307..121470189-chr3:121481888..121483548,2	MCF-7	breast:
3	chr3:121467372..121472022-chr3:121479274..121484300,4	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10934559	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs11706783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707518	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714406	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11715951	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716984	0.80[EUR][1000 genomes]
rs11717483	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719093	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719458	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11721291	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11721318	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs13061326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065245	0.80[GIH][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13072618	0.81[EUR][1000 genomes]
rs13072767	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074834	0.82[EUR][1000 genomes]
rs13083794	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13087578	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs13090798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098883	0.92[ASN][1000 genomes]
rs1318472	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13433692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573819	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17691170	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17742508	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1920320	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070180	0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs28674947	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33988592	0.82[EUR][1000 genomes]
rs34865234	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35359572	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35679661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35988617	0.82[EUR][1000 genomes]
rs3732408	0.82[EUR][1000 genomes]
rs3772128	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3772130	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs3805127	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4280673	0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298081	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4311252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55643643	0.81[EUR][1000 genomes]
rs55657471	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57636696	0.82[AMR][1000 genomes]
rs6768621	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769102	0.86[AMR][1000 genomes]
rs6776670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780302	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784571	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789736	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629369	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7631939	1.00[JPT][hapmap]
rs7649092	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9289177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812137	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9822949	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825248	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9826473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848027	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856641	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9878086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS 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	37 gene(s)	inside rSNPs	diseases
9	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs28660600	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs28660600	EAF2	cis	lymphoblastoid	seeQTL
rs28660600	HCLS1	cis	Whole Blood	GTEx
rs28660600	CHST13	cis	cerebellum	SCAN
rs28660600	HEG1	cis	parietal	SCAN
rs28660600	IQCB1	cis	Whole Blood	GTEx
rs28660600	IQCB1	cis	parietal	SCAN
rs28660600	SLC15A2	cis	cerebellum	SCAN
rs28660600	IQCB1	cis	cerebellum	SCAN
rs28660600	EAF2	cis	cerebellum	SCAN
rs28660600	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs28660600	PARP9	cis	cerebellum	SCAN
rs28660600	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121469400-121489200	Weak transcription	Aorta	Aorta
2	chr3:121469400-121489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:121476600-121485600	Weak transcription	Primary B cells from cord blood	blood
4	chr3:121476800-121485800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:121476800-121487400	Weak transcription	Dnd41	blood
6	chr3:121476800-121489200	Weak transcription	Spleen	Spleen
7	chr3:121477000-121487400	Weak transcription	HSMM	muscle
8	chr3:121477000-121487800	Weak transcription	Placenta	Placenta
9	chr3:121477200-121485600	Weak transcription	Lung	lung
10	chr3:121477200-121487600	Weak transcription	Left Ventricle	heart
11	chr3:121477200-121489000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:121477200-121494000	Weak transcription	Right Ventricle	heart
13	chr3:121477400-121487400	Weak transcription	Ovary	ovary
14	chr3:121477400-121487600	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:121478000-121499400	Weak transcription	HepG2	liver
16	chr3:121479200-121487400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:121479200-121489200	Weak transcription	HSMMtube	muscle
18	chr3:121480600-121488400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:121480800-121485600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:121482000-121487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:121482000-121489000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:121482400-121485400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:121482400-121489000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:121482600-121489000	Weak transcription	NH-A	brain
25	chr3:121482600-121489200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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