Variant report

Variant	rs41487846
Chromosome Location	chr15:40178504-40178505
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	chr15:40166842..40170366-chr15:40176074..40178554,3	MCF-7	breast:
2	chr15:40177423..40181071-chr15:40224799..40228084,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12373003	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28376567	0.86[ASN][1000 genomes]
rs28495043	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28573294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41497851	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923844	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4924399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55859027	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62002527	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62002531	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62002533	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62002534	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41487846	OIP5	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40162400-40187000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:40169600-40178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:40171600-40178600	Weak transcription	NH-A	brain
4	chr15:40174800-40178800	Weak transcription	NHLF	lung
5	chr15:40175200-40178600	Weak transcription	NHDF-Ad	bronchial
6	chr15:40176000-40178600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr15:40176000-40179000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr15:40176000-40180800	Enhancers	HMEC	breast
9	chr15:40176000-40182200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:40176000-40182600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr15:40176200-40180000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr15:40176200-40180600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:40176200-40182400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr15:40176200-40183800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:40176200-40185000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr15:40176400-40179200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:40176600-40179200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:40176800-40181000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:40177000-40180400	Weak transcription	Pancreas	Pancrea
20	chr15:40177000-40180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:40177000-40180800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:40177000-40183000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:40177200-40178600	Weak transcription	Osteobl	bone
24	chr15:40177200-40179400	Weak transcription	Stomach Mucosa	stomach
25	chr15:40177200-40179400	Weak transcription	HSMM	muscle
26	chr15:40177200-40179800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:40177200-40180200	Weak transcription	HSMMtube	muscle
28	chr15:40177400-40180400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:40177600-40179200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:40177800-40178600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr15:40177800-40179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:40177800-40180000	Weak transcription	Hela-S3	cervix
33	chr15:40178000-40179000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:40178000-40179400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:40178000-40179600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:40178000-40180200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr15:40178000-40181600	Enhancers	NHEK	skin
38	chr15:40178200-40179000	Weak transcription	Brain Anterior Caudate	brain
39	chr15:40178200-40179800	Weak transcription	Liver	Liver
40	chr15:40178400-40178600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr15:40178400-40179200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:40178400-40179400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:40178400-40179600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:40178400-40179800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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