Variant report

Variant	rs2553449
Chromosome Location	chr4:106698892-106698893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10025790	0.82[JPT][hapmap]
rs10516523	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11722731	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11934139	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11941690	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12639750	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1294670	0.91[ASN][1000 genomes]
rs1294673	0.91[ASN][1000 genomes]
rs13120110	0.93[ASN][1000 genomes]
rs13138544	0.85[CHD][hapmap]
rs13148869	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17036098	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17262764	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2044536	0.95[CHD][hapmap]
rs2080789	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2216517	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2544395	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2544405	0.82[ASN][1000 genomes]
rs2544412	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2544413	0.93[ASN][1000 genomes]
rs2553440	0.80[ASN][1000 genomes]
rs2553441	0.83[ASN][1000 genomes]
rs2553458	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2553462	0.98[ASN][1000 genomes]
rs2553468	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28628106	0.84[ASN][1000 genomes]
rs3756260	0.87[ASN][1000 genomes]
rs4699196	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6533218	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6820200	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7684839	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7685231	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs921113	0.82[JPT][hapmap]

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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv879700	chr4:106643445-106745057	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000947	chr4:106651153-106701679	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2553449	STEAP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106685400-106700000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:106687800-106699600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:106688400-106708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:106689200-106703600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:106689400-106706000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:106690800-106706000	Weak transcription	Fetal Heart	heart
7	chr4:106691400-106706400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:106692400-106729400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:106694000-106718200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:106694600-106704200	Weak transcription	HepG2	liver
11	chr4:106695200-106757000	Weak transcription	Primary B cells from cord blood	blood
12	chr4:106695600-106703000	Weak transcription	Thymus	Thymus
13	chr4:106697200-106725800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:106697800-106704200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:106697800-106723200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:106698000-106699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:106698000-106699200	Weak transcription	Fetal Stomach	stomach
18	chr4:106698000-106725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:106698200-106719200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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