Variant report

Variant	rs2856045
Chromosome Location	chr3:60545429-60545430
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	chr3:60540686..60542357-chr3:60544396..60547360,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1447960	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs151744	0.91[EUR][1000 genomes]
rs151749	1.00[YRI][hapmap]
rs1584339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1584340	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs171351	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs171352	0.87[EUR][1000 genomes]
rs181349	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2121854	0.87[EUR][1000 genomes]
rs2121856	0.87[EUR][1000 genomes]
rs241664	0.87[EUR][1000 genomes]
rs241666	0.95[EUR][1000 genomes]
rs241669	0.80[MKK][hapmap];1.00[YRI][hapmap]
rs241673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs241674	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs241676	0.91[EUR][1000 genomes]
rs241677	0.91[EUR][1000 genomes]
rs241678	0.91[EUR][1000 genomes]
rs241679	0.91[EUR][1000 genomes]
rs241680	0.91[EUR][1000 genomes]
rs241682	1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs241683	1.00[ASW][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs241684	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs241699	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs242185	0.87[EUR][1000 genomes]
rs242186	0.87[EUR][1000 genomes]
rs242188	0.87[EUR][1000 genomes]
rs2594259	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2594273	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682959	0.87[AFR][1000 genomes]
rs2682960	1.00[CEU][hapmap]
rs2682963	1.00[YRI][hapmap]
rs2682981	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682982	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2734362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2734368	1.00[YRI][hapmap]
rs2856011	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2856012	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2856013	0.87[AFR][1000 genomes]
rs2856015	0.87[AFR][1000 genomes]
rs6806175	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1008235	chr3:60388277-60558331	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv460569	chr3:60388322-60558331	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590399	chr3:60388322-60558331	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2763271	chr3:60391557-60558331	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv999284	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1002453	chr3:60391557-60558331	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv948513	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1008661	chr3:60397271-60558331	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1010907	chr3:60425237-60557503	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1002978	chr3:60425237-60558331	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1014064	chr3:60448591-60558331	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1000393	chr3:60461450-60558331	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv876856	chr3:60472815-60558331	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv876857	chr3:60472815-60558331	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv590403	chr3:60484433-60558331	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv876859	chr3:60519576-60558331	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv876860	chr3:60531242-60557685	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2856045	FABP4	trans	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60541200-60546200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:60542600-60546000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:60543200-60558800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:60543400-60548200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:60544400-60546200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:60545000-60545600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:60545000-60546200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:60545400-60546200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:60545400-60546600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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