Variant report

Variant	rs302563
Chromosome Location	chr6:39649567-39649568
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	chr6:39649513..39651387-chr6:39656055..39658420,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11752840	0.86[ASN][1000 genomes]
rs11754307	0.86[ASN][1000 genomes]
rs11754807	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs1380343	0.91[YRI][hapmap]
rs149242	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs149607	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1563770	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs159956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159957	0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs159958	0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs160019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160020	0.91[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs160021	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs160023	0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs160024	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs160028	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs160030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160032	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2199174	0.86[ASN][1000 genomes]
rs2446644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465672	1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2466410	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499450	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2499452	0.91[YRI][hapmap]
rs302548	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302559	0.94[AFR][1000 genomes]
rs302560	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302561	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302562	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs302564	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302573	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs302574	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs302575	0.98[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302579	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302586	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302587	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302588	0.91[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs302589	0.97[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302591	0.86[ASN][1000 genomes]
rs302592	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302593	0.91[ASW][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs302595	0.86[YRI][hapmap]
rs302596	0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs303653	0.91[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs303661	0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs303675	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs303677	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs303678	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs303693	0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs303699	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs303700	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs303701	0.91[ASW][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs55815613	0.86[ASN][1000 genomes]
rs55941685	0.86[ASN][1000 genomes]
rs56130116	0.86[ASN][1000 genomes]
rs62402464	0.86[ASN][1000 genomes]
rs62402465	0.86[ASN][1000 genomes]
rs62403334	0.86[ASN][1000 genomes]
rs62403359	0.86[ASN][1000 genomes]
rs62405160	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39637800-39651400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:39648000-39650000	Enhancers	Brain Cingulate Gyrus	brain
3	chr6:39648200-39650000	Enhancers	Brain Hippocampus Middle	brain
4	chr6:39648200-39650200	Enhancers	NHDF-Ad	bronchial
5	chr6:39648400-39649800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr6:39648400-39650200	Enhancers	Brain Substantia Nigra	brain
7	chr6:39649000-39650200	Enhancers	NHLF	lung
8	chr6:39649200-39650000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:39649200-39650000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:39649200-39650200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:39649200-39650200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:39649400-39649800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr6:39649400-39649800	Enhancers	NH-A	brain
14	chr6:39649400-39650000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:39649400-39650000	Enhancers	Brain Angular Gyrus	brain
16	chr6:39649400-39650200	Enhancers	Brain Anterior Caudate	brain
17	chr6:39649400-39653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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