Variant report

Variant	rs12490148
Chromosome Location	chr3:133523973-133523974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:133523861-133526079	SK-N-SH	brain:	n/a	n/a
2	TBL1XR1	chr3:133523950-133524737	K562	blood:	n/a	n/a
3	HCFC1	chr3:133523945-133525663	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:133380350..133382601-chr3:133523415..133526726,4	K562	blood:
2	chr3:133522634..133526763-chr3:133529104..133532905,8	K562	blood:
3	chr3:133523328..133525267-chr3:133529249..133532239,3	MCF-7	breast:
4	chr3:133523642..133526680-chr3:133527233..133530883,4	K562	blood:
5	chr3:133379614..133382648-chr3:133523517..133526970,4	MCF-7	breast:
6	chr3:133378019..133382399-chr3:133522860..133528810,6	K562	blood:
7	chr3:133523551..133526872-chr3:133527016..133531055,8	MCF-7	breast:

No data

Variant related genes	Relation type
SRPRB	TF binding region
ENSG00000242337	Chromatin interaction
ENSG00000144867	Chromatin interaction
ENSG00000163781	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11710936	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs12595	0.87[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs13079426	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1525889	0.84[CEU][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs1534165	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1830083	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1830084	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293375	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs35332919	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811647	0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs3811658	0.81[CHB][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap]
rs4854760	0.84[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4854761	0.84[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4854762	0.81[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57847564	0.80[ASN][1000 genomes]
rs58851383	0.80[ASN][1000 genomes]
rs6794945	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73217233	0.86[ASN][1000 genomes]
rs7638018	0.84[CEU][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs8177224	0.91[MEX][hapmap]
rs8177240	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs8177248	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs8177252	0.84[CEU][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap]
rs8177253	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs8177262	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs8177272	0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs9813689	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9843728	0.88[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs9871148	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9882812	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS 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 target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv4018	chr3:133485867-133530668	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12490148	SRPRB	cis	parietal	SCAN
rs12490148	TF,SRPRB	cis	brain	BrainEAC
rs12490148	TOPBP1	cis	parietal	SCAN
rs12490148	TF,SRPRB	cis	intralobular white matter	BrainEAC
rs12490148	TF,SRPRB	cis	inferior olivary nucleus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133519200-133524000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:133519200-133524000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:133519600-133524000	Weak transcription	HMEC	breast
4	chr3:133519800-133524000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:133521600-133524000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:133522400-133524000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:133522600-133524000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:133523800-133524000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:133523800-133524000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:133523800-133524000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:133523800-133524000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:133523800-133524000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:133523800-133524000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:133523800-133524000	Active TSS	Brain Angular Gyrus	brain
15	chr3:133523800-133524000	Enhancers	Brain Anterior Caudate	brain
16	chr3:133523800-133524000	Enhancers	Brain Hippocampus Middle	brain
17	chr3:133523800-133524000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:133523800-133524000	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:133523800-133524000	Enhancers	A549	lung
20	chr3:133523800-133524000	Enhancers	Dnd41	blood
21	chr3:133523800-133524000	Enhancers	NHEK	skin
22	chr3:133523800-133524200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:133523800-133524200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr3:133523800-133524200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:133523800-133524200	Active TSS	HepG2	liver
26	chr3:133523800-133524400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:133523800-133525200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr3:133523800-133525200	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr3:133523800-133525600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:133523800-133526000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:133523800-133526800	Active TSS	Pancreatic Islets	Pancreatic Islet

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