Variant report

Variant	rs4924570
Chromosome Location	chr15:41974660-41974661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41973132..41976112-chr15:41981516..41983125,2	K562	blood:
2	chr15:41954590..41956853-chr15:41972603..41974738,2	K562	blood:
3	chr15:41952625..41954330-chr15:41973061..41975209,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1105881	0.85[JPT][hapmap]
rs11070343	0.82[ASN][1000 genomes]
rs1107858	0.92[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634956	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11637341	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440747	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1531140	0.92[JPT][hapmap]
rs16952372	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs16971976	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs17676742	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs17677199	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17677991	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17678138	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17678552	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17678767	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs17734856	0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs1918310	0.86[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs2004162	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241522	0.88[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2277535	1.00[ASW][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs2278964	1.00[ASW][hapmap]
rs2303516	0.92[JPT][hapmap]
rs2303518	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs2305654	0.85[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs2412622	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2577960	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28444909	0.88[EUR][1000 genomes]
rs28556632	0.93[ASN][1000 genomes]
rs28700954	0.81[ASN][1000 genomes]
rs28810086	0.93[ASN][1000 genomes]
rs28850384	0.93[ASN][1000 genomes]
rs3743024	1.00[ASW][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs4923905	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4923914	0.85[JPT][hapmap]
rs4924564	0.93[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4924575	1.00[ASW][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs4924576	1.00[ASW][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs62002066	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003900	0.93[ASN][1000 genomes]
rs8035855	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs890498	0.83[JPT][hapmap];0.81[AFR][1000 genomes]
rs9672298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9672360	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4924570	SPTBN5	cis	cerebellum	SCAN
rs4924570	MGA	cis	lesional skin	skin_eQTL
rs4924570	MAPKBP1	cis	cerebellum	SCAN
rs4924570	RPAP1	cis	parietal	SCAN
rs4924570	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs4924570	NDUFAF1	cis	parietal	SCAN
rs4924570	JMJD7-PLA2G4B	cis	parietal	SCAN
rs4924570	JMJD7-PLA2G4B	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954400-41978600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
3	chr15:41954600-41976200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
5	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
6	chr15:41954800-41976200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:41954800-41980800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:41958400-41978400	Weak transcription	Pancreas	Pancrea
10	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
12	chr15:41959600-41981000	Weak transcription	Osteobl	bone
13	chr15:41961600-41975400	Weak transcription	Aorta	Aorta
14	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:41962000-41980200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:41962000-41983800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
18	chr15:41962000-41990800	Weak transcription	NH-A	brain
19	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:41962000-42001400	Weak transcription	Gastric	stomach
21	chr15:41962200-41974800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:41962200-41984400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:41962600-41981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:41962600-41981800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:41962600-41983400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:41962600-41983600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:41962600-41984000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:41962600-41988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:41963400-41988400	Weak transcription	Placenta	Placenta
31	chr15:41963600-41987800	Weak transcription	Primary B cells from cord blood	blood
32	chr15:41964400-41975800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:41964600-41981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:41964600-41982200	Weak transcription	Ovary	ovary
35	chr15:41964800-41974800	Weak transcription	Primary T cells from cord blood	blood
36	chr15:41964800-41983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:41965000-41980600	Weak transcription	K562	blood
38	chr15:41965000-41982400	Weak transcription	Brain Anterior Caudate	brain
39	chr15:41966600-41984400	Weak transcription	Left Ventricle	heart
40	chr15:41966600-41988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:41967600-41976400	Weak transcription	A549	lung
42	chr15:41967600-41976400	Weak transcription	HepG2	liver
43	chr15:41967600-41982600	Weak transcription	GM12878-XiMat	blood
44	chr15:41967800-41980600	Weak transcription	Dnd41	blood
45	chr15:41968200-41974800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr15:41968400-41975400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:41968400-41982200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:41968800-41988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:41969600-41974800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr15:41970600-41976600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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