Variant report

Variant	rs4924556
Chromosome Location	chr15:41878208-41878209
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41407897..41409667-chr15:41876461..41878858,2	MCF-7	breast:
2	chr15:41757459..41758345-chr15:41877423..41878368,2	MCF-7	breast:
3	chr15:41855197..41857577-chr15:41876968..41879367,2	K562	blood:
4	chr15:41848431..41851205-chr15:41877401..41879696,2	K562	blood:

Variant related genes	Relation type
ENSG00000259838	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10438299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1077714	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906912	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12915829	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246444	0.92[CEU][hapmap];0.85[CHB][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2277537	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2289743	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs2482307	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28655000	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28792443	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28844285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784283	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924552	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924554	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924559	0.92[ASN][1000 genomes]
rs6493004	0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs6493005	0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs66906913	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68058196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7166371	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7183231	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025165	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4924556	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs4924556	ZSCAN29	cis	cerebellum	SCAN
rs4924556	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs4924556	C15orf41	cis	cerebellum	SCAN
rs4924556	BMF	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41877200-41878400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:41877200-41878400	Enhancers	Fetal Heart	heart
3	chr15:41877400-41878400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:41877400-41878400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr15:41877400-41878400	Active TSS	Fetal Lung	lung
6	chr15:41877600-41878400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:41878000-41878400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:41878000-41881000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:41878200-41878400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr15:41878200-41878400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr15:41878200-41878400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:41878200-41878400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:41878200-41878400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr15:41878200-41878400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr15:41878200-41878400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr15:41878200-41878400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr15:41878200-41878400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:41878200-41878400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr15:41878200-41878400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:41878200-41878400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:41878200-41878400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:41878200-41878400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:41878200-41878400	Enhancers	Liver	Liver
24	chr15:41878200-41878400	Enhancers	Brain Anterior Caudate	brain
25	chr15:41878200-41878400	Flanking Active TSS	Fetal Kidney	kidney
26	chr15:41878200-41878400	Active TSS	Fetal Muscle Trunk	muscle
27	chr15:41878200-41878400	Enhancers	Fetal Muscle Leg	muscle
28	chr15:41878200-41878400	Enhancers	Placenta	Placenta
29	chr15:41878200-41878400	Enhancers	HepG2	liver
30	chr15:41878200-41878400	Enhancers	HMEC	breast
31	chr15:41878200-41878400	Enhancers	HUVEC	blood vessel
32	chr15:41878200-41878400	Enhancers	NHDF-Ad	bronchial
33	chr15:41878200-41878400	Active TSS	NHEK	skin
34	chr15:41878200-41878400	Enhancers	NHLF	lung
35	chr15:41878200-41878600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:41878200-41878800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:41878200-41879200	Enhancers	Fetal Intestine Large	intestine
38	chr15:41878200-41879200	Enhancers	Fetal Intestine Small	intestine
39	chr15:41878200-41879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:41878200-41880600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:41878200-41882600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:41878200-41882600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:41878200-41885600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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