Variant report

Variant	rs2713749
Chromosome Location	chr3:100699560-100699561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:201738761..201739494-chr3:100699132..100700073,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1036468	0.88[CHB][hapmap]
rs13085823	0.90[ASN][1000 genomes]
rs1375512	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449299	1.00[ASN][1000 genomes]
rs1530731	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1579969	0.90[ASN][1000 genomes]
rs16843153	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17338729	0.88[CHB][hapmap]
rs17339226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17340282	0.81[ASN][1000 genomes]
rs1836985	0.86[CHB][hapmap]
rs2245370	0.88[CHB][hapmap]
rs2252229	0.88[CHB][hapmap]
rs2576370	0.88[CHB][hapmap]
rs2576384	0.88[CHB][hapmap]
rs2576385	0.88[CHB][hapmap]
rs2576389	0.88[CHB][hapmap]
rs2595907	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2713758	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713759	0.88[CHB][hapmap]
rs2713762	0.88[CHB][hapmap]
rs2713794	0.88[CHB][hapmap]
rs2713798	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs55687619	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936420	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56077494	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56237429	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57194842	0.80[EUR][1000 genomes]
rs59476872	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6774218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787197	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6787878	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141447	0.81[ASN][1000 genomes]
rs73143038	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73143044	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73143061	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143062	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143064	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143072	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144908	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144910	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144915	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144970	0.90[ASN][1000 genomes]
rs73149160	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7609734	0.88[CHB][hapmap]
rs7621518	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7623956	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637274	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7641631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643050	0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7646218	0.88[CHB][hapmap]
rs959713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2713749	ST3GAL6	cis	cerebellum	SCAN
rs2713749	ABI3BP	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100688400-100701800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:100692000-100700200	Weak transcription	HSMM	muscle
3	chr3:100692200-100701400	Weak transcription	Fetal Lung	lung
4	chr3:100692600-100711200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:100693000-100700400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:100694800-100700000	Weak transcription	Ovary	ovary
7	chr3:100696200-100702200	Enhancers	Fetal Stomach	stomach
8	chr3:100697800-100699600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:100698000-100699600	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:100698000-100699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:100698000-100699800	Weak transcription	HSMMtube	muscle
12	chr3:100698000-100700000	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:100698000-100700000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:100698000-100701600	Weak transcription	Psoas Muscle	Psoas
15	chr3:100698200-100699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:100698200-100699800	Weak transcription	NHDF-Ad	bronchial
17	chr3:100698400-100701400	Weak transcription	NHLF	lung
18	chr3:100698600-100700000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:100698600-100700600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:100698800-100700200	Weak transcription	Osteobl	bone

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