Variant report

Variant	rs3774491
Chromosome Location	chr3:53663835-53663836
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	chr3:53661729..53666678-chr3:53666737..53670217,5	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1037827	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1380606	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1401494	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1599230	0.81[CEU][hapmap]
rs1841291	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1870564	0.84[CHB][hapmap]
rs2250736	0.85[CEU][hapmap];0.81[GIH][hapmap];0.82[EUR][1000 genomes]
rs2612022	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2633707	0.89[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2680654	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2680656	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3774481	0.92[CEU][hapmap]
rs3774486	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3821854	0.94[JPT][hapmap]
rs6445590	0.90[CEU][hapmap]
rs6445591	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786135	1.00[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6803827	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs754063	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7630805	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs898411	0.84[CHB][hapmap]
rs898415	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs898416	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs930949	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9846874	0.81[CEU][hapmap]
rs9850569	0.92[CEU][hapmap]
rs9883910	0.90[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3774491	IQCF1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53652800-53684000	Weak transcription	Right Atrium	heart
2	chr3:53659400-53664600	Weak transcription	Fetal Kidney	kidney
3	chr3:53661400-53667200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:53661600-53665000	Weak transcription	Fetal Intestine Small	intestine
5	chr3:53662000-53665400	Enhancers	Stomach Mucosa	stomach
6	chr3:53662200-53664000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:53662200-53664200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:53662200-53664800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53662200-53664800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:53662400-53664400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:53662600-53664200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:53663400-53664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:53663400-53665000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:53663600-53664000	Weak transcription	Fetal Lung	lung
15	chr3:53663600-53664000	Enhancers	Gastric	stomach
16	chr3:53663600-53664200	Enhancers	Pancreas	Pancrea
17	chr3:53663600-53664600	Weak transcription	HMEC	breast
18	chr3:53663800-53664800	Weak transcription	Esophagus	oesophagus

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