Variant report

Variant	rs9880088
Chromosome Location	chr3:49178990-49178991
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	chr3:49057782..49059495-chr3:49177436..49179883,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207605	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000178149	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10049462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10154895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11130182	0.88[ASN][1000 genomes]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710247	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11712006	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11716334	0.87[ASN][1000 genomes]
rs11716614	0.92[CEU][hapmap]
rs11718982	0.91[EUR][1000 genomes]
rs11719220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719457	0.84[EUR][1000 genomes]
rs11720460	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.90[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12493001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	1.00[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12715434	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13064784	0.85[ASN][1000 genomes]
rs13068038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13072554	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13080725	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086240	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs13087930	0.84[EUR][1000 genomes]
rs13090839	0.84[EUR][1000 genomes]
rs13096406	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13315711	1.00[JPT][hapmap]
rs13321689	1.00[ASW][hapmap]
rs13324117	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs28690891	0.81[AFR][1000 genomes]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34326553	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34343820	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34504524	0.86[EUR][1000 genomes]
rs34509487	0.84[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34784192	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34889065	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35102816	0.86[EUR][1000 genomes]
rs35108630	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35673421	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3923475	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4308307	0.92[ASN][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4499638	0.97[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4536858	0.97[ASN][1000 genomes]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4955418	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974078	0.87[CHD][hapmap]
rs4974080	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4974082	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55713230	0.97[ASN][1000 genomes]
rs55921200	0.81[EUR][1000 genomes]
rs56306491	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56318350	0.84[EUR][1000 genomes]
rs61583136	0.95[ASN][1000 genomes]
rs61729488	0.82[EUR][1000 genomes]
rs62262517	0.83[ASN][1000 genomes]
rs6414613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446205	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67286839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6770112	0.95[ASN][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6781790	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6784111	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6790914	0.97[ASN][1000 genomes]
rs6794924	0.87[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs71324929	0.82[EUR][1000 genomes]
rs71324939	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73084135	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430198	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7432989	1.00[CHD][hapmap]
rs7615235	0.82[ASN][1000 genomes]
rs7621015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7628719	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7643368	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9311440	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9811724	1.00[ASW][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826085	1.00[ASW][hapmap]
rs9826525	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9828310	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9835439	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs9844757	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs9846123	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9848772	1.00[YRI][hapmap]
rs9850917	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9855123	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9862483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873994	0.85[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs9880309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv3343248	chr3:49177848-49180746	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9880088	LRRC2	cis	cerebellum	SCAN
rs9880088	HEMK1	cis	parietal	SCAN
rs9880088	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9880088	CCDC36	cis	cerebellum	SCAN
rs9880088	ALAS1	cis	cerebellum	SCAN
rs9880088	CSPG5	cis	parietal	SCAN
rs9880088	CCDC71	cis	cerebellum	SCAN
rs9880088	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9880088	KBTBD3	trans	parietal	SCAN
rs9880088	WDR6	cis	Artery Tibial	GTEx
rs9880088	NICN1	cis	cerebellum	SCAN
rs9880088	RNF123	cis	parietal	SCAN
rs9880088	WDR6	cis	Adipose Subcutaneous	GTEx
rs9880088	ARIH2	cis	cerebellum	SCAN
rs9880088	WDR6	cis	cerebellum	SCAN
rs9880088	WDR6	cis	Esophagus Mucosa	GTEx
rs9880088	C3orf62	cis	cerebellum	SCAN
rs9880088	WDR6	cis	parietal	SCAN
rs9880088	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49171600-49179000	Weak transcription	Thymus	Thymus
2	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:49174000-49179200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:49177800-49179000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:49177800-49179000	Weak transcription	Esophagus	oesophagus
6	chr3:49178800-49179200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:49178800-49179400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49178800-49179600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
9	chr3:49178800-49179600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:49178800-49179800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:49178800-49179800	ZNF genes & repeats	Placenta	Placenta

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