Variant report

Variant	rs11259948
Chromosome Location	chr15:83461261-83461262
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	chr15:83456831..83459102-chr15:83459317..83461844,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1105288	0.91[CHB][hapmap]
rs1109373	0.86[CHB][hapmap]
rs11259947	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11259949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11259952	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs11856878	0.82[YRI][hapmap]
rs1271044	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs12902970	0.87[EUR][1000 genomes]
rs12903411	0.85[EUR][1000 genomes]
rs12907913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910606	0.86[MKK][hapmap];0.80[YRI][hapmap]
rs12913102	0.80[AMR][1000 genomes]
rs1533136	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1971555	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2379996	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2890314	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4260027	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs66500181	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66851469	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8025432	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8028133	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[MKK][hapmap]
rs8033573	0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap]
rs8033726	0.82[LWK][hapmap]
rs8041231	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs8042254	0.83[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11259948	MEX3B	cis	parietal	SCAN
rs11259948	EFTUD1	cis	cerebellum	SCAN
rs11259948	WHAMM	cis	Adipose Subcutaneous	GTEx
rs11259948	BTBD1	cis	cerebellum	SCAN
rs11259948	WHDC1	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83434800-83462200	Weak transcription	Ovary	ovary
2	chr15:83436400-83467800	Weak transcription	Psoas Muscle	Psoas
3	chr15:83440800-83468000	Weak transcription	Right Ventricle	heart
4	chr15:83450400-83477600	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:83455600-83467400	Weak transcription	Fetal Heart	heart
6	chr15:83456000-83468200	Weak transcription	Left Ventricle	heart
7	chr15:83456200-83464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:83456200-83467800	Weak transcription	Fetal Muscle Leg	muscle
9	chr15:83460200-83461600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:83460200-83461600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:83460400-83461600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:83460400-83461800	Enhancers	HMEC	breast
13	chr15:83460400-83462200	Enhancers	NHEK	skin
14	chr15:83461000-83464200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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