Variant report

Variant	rs12485978
Chromosome Location	chr3:46165809-46165810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46165088..46167964-chr3:46179525..46182500,2	MCF-7	breast:
2	chr3:46162316..46164554-chr3:46164815..46166918,2	K562	blood:
3	chr3:46165710..46167302-chr3:46203883..46205469,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11130080	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11130085	0.89[ASN][1000 genomes]
rs11130086	0.90[ASN][1000 genomes]
rs1118879	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917890	0.89[ASN][1000 genomes]
rs11929281	0.89[ASN][1000 genomes]
rs12496322	0.89[ASN][1000 genomes]
rs12629632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630101	0.82[JPT][hapmap]
rs12635657	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs12637023	0.88[ASN][1000 genomes]
rs12639598	0.82[JPT][hapmap]
rs13060901	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13065737	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073861	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13077099	0.89[ASN][1000 genomes]
rs13077923	0.93[ASN][1000 genomes]
rs13078053	0.92[ASN][1000 genomes]
rs13082280	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13098271	0.87[EUR][1000 genomes]
rs13320534	0.88[YRI][hapmap]
rs13434029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13434336	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1392290	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1491959	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491960	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1546077	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546078	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1602579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604069	0.92[ASN][1000 genomes]
rs17078577	0.88[ASN][1000 genomes]
rs1909595	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1909596	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976366	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976367	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994490	0.82[JPT][hapmap]
rs2131091	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2220678	0.90[ASN][1000 genomes]
rs2373150	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373153	0.91[ASN][1000 genomes]
rs2373154	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs34067839	0.93[ASN][1000 genomes]
rs34906043	0.88[EUR][1000 genomes]
rs35359253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35435608	0.88[EUR][1000 genomes]
rs35462017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35567508	0.92[ASN][1000 genomes]
rs35657218	0.88[EUR][1000 genomes]
rs36111470	0.93[ASN][1000 genomes]
rs3733100	0.82[JPT][hapmap]
rs3796375	0.82[JPT][hapmap]
rs3821884	0.82[JPT][hapmap]
rs3851347	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs4318588	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682806	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682809	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683175	0.88[ASN][1000 genomes]
rs4683178	0.89[ASN][1000 genomes]
rs56307311	0.93[ASN][1000 genomes]
rs59521415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61079448	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441944	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764042	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6776028	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6780163	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs6784214	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794103	0.89[ASN][1000 genomes]
rs6794475	0.91[ASN][1000 genomes]
rs6795629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800484	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805094	0.83[EUR][1000 genomes]
rs6809381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730983	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs737452	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs751552	0.82[JPT][hapmap]
rs751553	0.82[JPT][hapmap]
rs7610518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623190	0.81[EUR][1000 genomes]
rs7623460	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7631598	0.81[ASN][1000 genomes]
rs7642701	0.88[EUR][1000 genomes]
rs9311386	0.92[ASN][1000 genomes]
rs9311387	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9637425	0.88[ASN][1000 genomes]
rs9824886	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9849015	0.82[EUR][1000 genomes]
rs9870445	0.92[ASN][1000 genomes]
rs9876587	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9990063	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12485978	ANO10	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46156800-46168000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:46157200-46166600	Weak transcription	Psoas Muscle	Psoas
3	chr3:46157200-46168600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:46161400-46169400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:46162800-46168800	Weak transcription	HMEC	breast
6	chr3:46163200-46166600	Enhancers	NHLF	lung
7	chr3:46163200-46166800	Enhancers	Fetal Stomach	stomach
8	chr3:46164000-46171000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:46164400-46166400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:46164400-46166800	Enhancers	Placenta	Placenta
11	chr3:46164800-46167000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:46165000-46166000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr3:46165000-46166800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:46165000-46167000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:46165000-46167000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:46165000-46167000	Enhancers	Adipose Nuclei	Adipose
17	chr3:46165200-46166000	Enhancers	Spleen	Spleen
18	chr3:46165200-46166200	Enhancers	Hela-S3	cervix
19	chr3:46165200-46166600	Enhancers	Ovary	ovary
20	chr3:46165200-46166800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:46165400-46166000	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:46165400-46166200	Enhancers	Primary B cells from cord blood	blood
23	chr3:46165400-46166400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:46165400-46166400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:46165400-46166600	Enhancers	NHDF-Ad	bronchial
26	chr3:46165400-46170800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:46165600-46166800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:46165800-46167000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:46165800-46167000	Enhancers	Fetal Lung	lung
30	chr3:46165800-46168600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:46165800-46169000	Weak transcription	Dnd41	blood

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