Variant report

Variant	rs6772441
Chromosome Location	chr3:118676806-118676807
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	chr3:118675897..118678259-chr3:118679117..118681449,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1158699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492855	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495725	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496820	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435655	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs16829179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160054	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28565574	0.80[AFR][1000 genomes]
rs28573387	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28592657	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821882	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611809	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56728928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58284747	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773865	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs6779428	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6795721	0.87[ASW][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs6796798	0.84[MKK][hapmap]
rs6807110	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs6807838	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968605	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968610	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968613	0.83[AFR][1000 genomes]
rs72968638	0.82[AFR][1000 genomes]
rs7633584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811829	0.82[AFR][1000 genomes]
rs9817943	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821022	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821458	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826100	0.82[YRI][hapmap]
rs9828087	0.83[AFR][1000 genomes]
rs9828870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833229	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836642	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849421	0.83[AFR][1000 genomes]
rs9855713	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873807	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[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];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874337	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6772441	NCAPD2	trans	brain	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118662000-118679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:118662000-118679800	Weak transcription	Ovary	ovary
3	chr3:118666200-118677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:118669200-118677600	Weak transcription	Brain Angular Gyrus	brain
5	chr3:118672800-118677000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:118673000-118677200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:118673200-118677200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:118675400-118677200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:118675400-118677200	Enhancers	Brain Hippocampus Middle	brain
10	chr3:118675400-118680800	Enhancers	Brain Anterior Caudate	brain
11	chr3:118675600-118677200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:118675600-118684800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:118676000-118677800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:118676000-118678000	Enhancers	Primary T cells from cord blood	blood
15	chr3:118676200-118677000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr3:118676200-118677200	Weak transcription	Brain Substantia Nigra	brain
17	chr3:118676400-118677000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:118676600-118678200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:118676800-118677600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:118676800-118677800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:118676800-118679800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:118676800-118684000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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