Variant report

Variant	rs4886406
Chromosome Location	chr15:75057203-75057204
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75052612..75054479-chr15:75056291..75058590,3	K562	blood:
2	chr15:75056268..75058478-chr15:75059962..75062462,2	K562	blood:
3	chr15:75055933..75058709-chr15:75257513..75259358,2	K562	blood:
4	chr15:75056268..75058478-chr15:75059962..75062607,3	K562	blood:
5	chr15:74726274..74728760-chr15:75055542..75058469,2	K562	blood:

Variant related genes	Relation type
ENSG00000138623	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072502	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072504	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072505	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072506	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11072508	0.82[CEU][hapmap]
rs11634474	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs11854147	0.82[CEU][hapmap]
rs12442901	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12591078	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1378938	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs1543927	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2168519	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2301249	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs2445618	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2472298	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2472299	0.86[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2472300	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784790	0.82[EUR][1000 genomes]
rs4886615	0.81[MKK][hapmap]
rs4886619	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap]
rs4886629	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs60001770	0.83[ASN][1000 genomes]
rs7085	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[MKK][hapmap]
rs7162232	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap]
rs7176022	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs7180484	0.91[CEU][hapmap]
rs72730503	0.80[EUR][1000 genomes]
rs762551	0.86[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033381	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9210	0.82[CEU][hapmap]
rs936226	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs936228	0.81[MKK][hapmap]
rs936229	0.81[MKK][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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886406	MPI	cis	multi-tissue	Pritchard
rs4886406	SCAMP5	cis	cerebellum	SCAN
rs4886406	SCAMP2	cis	parietal	SCAN
rs4886406	MPI	cis	lymphoblastoid	seeQTL
rs4886406	NEO1	cis	parietal	SCAN
rs4886406	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75044800-75062600	Weak transcription	Right Atrium	heart
2	chr15:75047200-75063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:75054800-75060600	Weak transcription	HepG2	liver
4	chr15:75055200-75063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:75055400-75061000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:75055600-75060600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:75055600-75061000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:75055600-75061000	Weak transcription	HUVEC	blood vessel
9	chr15:75055600-75065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:75056000-75060800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:75056000-75061000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:75056000-75061000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75056000-75061000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:75056000-75069000	Weak transcription	Lung	lung
15	chr15:75056200-75060400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:75056200-75061000	Weak transcription	HMEC	breast
17	chr15:75056200-75063200	Weak transcription	Spleen	Spleen
18	chr15:75056400-75059800	Weak transcription	Placenta	Placenta
19	chr15:75056400-75059800	Weak transcription	NHEK	skin
20	chr15:75056400-75060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:75056400-75060000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:75056400-75061000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:75056400-75061000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:75056400-75061000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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