Variant report

Variant	rs523246
Chromosome Location	chr11:34845011-34845012
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34804567..34805318-chr11:34844825..34845441,2	MCF-7	breast:
2	chr11:34844808..34847036-chr11:34936903..34938822,2	MCF-7	breast:
3	chr11:34828810..34832933-chr11:34843194..34845330,4	K562	blood:
4	chr11:34842739..34845478-chr11:34850745..34855445,5	K562	blood:
5	chr11:34843450..34845842-chr11:34860291..34863263,2	MCF-7	breast:
6	chr11:34842739..34845478-chr11:34850745..34852708,3	K562	blood:
7	chr11:34686698..34687242-chr11:34844773..34845279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110435	Chromatin interaction
ENSG00000149089	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10501136	0.91[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1097517	0.89[ASN][1000 genomes]
rs11602870	0.82[EUR][1000 genomes]
rs11602886	0.80[EUR][1000 genomes]
rs11605381	0.81[EUR][1000 genomes]
rs12278295	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs12291580	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2915186	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2956073	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34026463	0.82[EUR][1000 genomes]
rs34878924	0.82[EUR][1000 genomes]
rs35833762	0.82[EUR][1000 genomes]
rs35953213	0.81[EUR][1000 genomes]
rs473848	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs473885	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs485845	0.90[ASN][1000 genomes]
rs490410	0.82[AFR][1000 genomes]
rs498798	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs502857	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs504186	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs508062	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512013	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514220	0.80[AFR][1000 genomes]
rs525202	0.88[EUR][1000 genomes]
rs537873	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547504	0.99[ASN][1000 genomes]
rs548967	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs550313	0.90[ASN][1000 genomes]
rs552171	0.90[ASN][1000 genomes]
rs561477	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566798	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs568529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571164	0.83[AFR][1000 genomes]
rs579926	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61881103	0.82[EUR][1000 genomes]
rs61881104	0.82[EUR][1000 genomes]
rs61881107	0.81[EUR][1000 genomes]
rs7131074	0.82[EUR][1000 genomes]
rs7946699	0.82[EUR][1000 genomes]
rs7946980	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs836950	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs523246	APIP	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34832400-34846000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:34843600-34845600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:34843600-34845600	Enhancers	Liver	Liver
4	chr11:34843800-34845800	Enhancers	Adipose Nuclei	Adipose
5	chr11:34844000-34845800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:34844400-34846200	Enhancers	HepG2	liver
7	chr11:34844400-34847800	Enhancers	Brain Angular Gyrus	brain
8	chr11:34844600-34846400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:34844800-34845200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:34844800-34845200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:34844800-34845400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:34844800-34845600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:34844800-34845600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:34844800-34846000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr11:34844800-34846600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:34844800-34847600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr11:34844800-34848000	Enhancers	Brain Anterior Caudate	brain
18	chr11:34844800-34848000	Enhancers	Brain Hippocampus Middle	brain
19	chr11:34844800-34848200	Enhancers	Brain Cingulate Gyrus	brain
20	chr11:34844800-34848200	Enhancers	Brain Substantia Nigra	brain
21	chr11:34844800-34849400	Enhancers	Stomach Mucosa	stomach
22	chr11:34845000-34845200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:34845000-34845200	Enhancers	Esophagus	oesophagus
24	chr11:34845000-34845200	Enhancers	K562	blood
25	chr11:34845000-34845800	Enhancers	Fetal Muscle Leg	muscle
26	chr11:34845000-34846200	Enhancers	Right Atrium	heart
27	chr11:34845000-34846800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:34845000-34849400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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