Variant report

Variant	rs12441675
Chromosome Location	chr15:83611362-83611363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83586586..83589404-chr15:83610320..83612935,3	MCF-7	breast:
2	chr15:83611228..83613735-chr15:83667947..83669649,2	MCF-7	breast:
3	chr15:83610269..83612055-chr15:83875374..83877470,2	MCF-7	breast:
4	chr15:83604502..83607500-chr15:83609162..83613049,3	K562	blood:
5	chr15:83610228..83612890-chr15:83652094..83656198,6	MCF-7	breast:
6	chr15:83254004..83256301-chr15:83611241..83613482,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166503	Chromatin interaction
ENSG00000103942	Chromatin interaction
ENSG00000169612	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1037403	0.95[JPT][hapmap]
rs11259960	1.00[JPT][hapmap]
rs12050725	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12148275	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568657	0.89[JPT][hapmap]
rs2046070	0.94[JPT][hapmap]
rs2061947	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2123157	0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs2123158	0.81[AMR][1000 genomes]
rs2167602	0.94[JPT][hapmap]
rs4842917	0.93[ASN][1000 genomes]
rs4842935	0.94[JPT][hapmap]
rs4843141	1.00[JPT][hapmap]
rs4843144	0.80[JPT][hapmap]
rs4843146	0.93[JPT][hapmap]
rs6603041	0.94[JPT][hapmap]
rs8034220	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8043020	0.94[JPT][hapmap]
rs872598	0.80[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs872599	0.81[CEU][hapmap];0.94[JPT][hapmap]

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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12441675	C15orf40	cis	normal skin	skin_eQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83586600-83619400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:83588800-83611600	Weak transcription	Right Atrium	heart
3	chr15:83606200-83611600	Weak transcription	A549	lung
4	chr15:83606600-83613200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:83606600-83618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:83606600-83620000	Weak transcription	Right Ventricle	heart
7	chr15:83606800-83611400	Weak transcription	HSMMtube	muscle
8	chr15:83606800-83611600	Weak transcription	Left Ventricle	heart
9	chr15:83609000-83613800	Enhancers	Pancreas	Pancrea
10	chr15:83610200-83611400	Enhancers	Esophagus	oesophagus
11	chr15:83610200-83612600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:83610400-83612400	Enhancers	HMEC	breast
13	chr15:83610600-83612200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:83610600-83612200	Enhancers	Liver	Liver
15	chr15:83610600-83612200	Enhancers	NHEK	skin
16	chr15:83610600-83613800	Enhancers	Gastric	stomach
17	chr15:83610600-83614200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:83610800-83611400	Enhancers	Psoas Muscle	Psoas
19	chr15:83610800-83612400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:83611000-83611400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr15:83611000-83612000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:83611000-83612000	Enhancers	Placenta	Placenta
23	chr15:83611000-83612200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:83611000-83612200	Enhancers	Lung	lung
25	chr15:83611200-83611600	Enhancers	NH-A	brain
26	chr15:83611200-83612000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:83611200-83612000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:83611200-83612000	Enhancers	Hela-S3	cervix
29	chr15:83611200-83612000	Enhancers	Osteobl	bone
30	chr15:83611200-83612200	Enhancers	HSMM	muscle
31	chr15:83611200-83614400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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