Variant report

Variant	rs4680254
Chromosome Location	chr3:150946047-150946048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150945162..150946781-chr3:151000301..151001339,9	K562	blood:
2	chr3:150945207..150946162-chr3:151045062..151046047,6	K562	blood:
3	chr3:150945248..150946199-chr3:151000415..151001358,11	MCF-7	breast:
4	chr3:150945446..150946139-chr3:151635662..151636300,2	K562	blood:
5	chr22:50714274..50714813-chr3:150945496..150946124,2	MCF-7	breast:
6	chr3:150945296..150946248-chr3:150999366..150999969,2	MCF-7	breast:
7	chr3:150945279..150946102-chr3:151045158..151045936,2	MCF-7	breast:
8	chr3:150945195..150946190-chr3:151556389..151557005,2	K562	blood:

No data

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10212582	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1048408	0.82[CEU][hapmap]
rs10513392	0.82[CEU][hapmap]
rs11711104	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11719936	0.82[CEU][hapmap]
rs13317873	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1472122	0.82[CEU][hapmap]
rs1565574	0.85[CEU][hapmap]
rs1882014	0.82[CEU][hapmap]
rs1882015	0.82[CEU][hapmap]
rs1882016	0.82[CEU][hapmap]
rs1920395	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1980143	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2904430	0.82[CEU][hapmap]
rs3846072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4269062	0.82[EUR][1000 genomes]
rs4679772	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680257	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440730	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6782715	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6807308	0.89[CEU][hapmap]
rs6809692	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73021201	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617677	0.89[CEU][hapmap]
rs7621113	0.81[AMR][1000 genomes]
rs7621183	0.86[AMR][1000 genomes]
rs7621211	0.81[AMR][1000 genomes]
rs7623448	0.81[AMR][1000 genomes]
rs7653603	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs8180086	0.82[CEU][hapmap]
rs9757688	0.81[AMR][1000 genomes]
rs9810067	0.82[CEU][hapmap]
rs9815520	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9827619	0.82[CEU][hapmap]
rs9828553	0.82[CEU][hapmap]
rs9835328	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9853297	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9870740	0.89[CEU][hapmap]
rs9875152	0.82[CEU][hapmap]
rs9880339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680254	CPB1	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150928800-150946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:150928800-150952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:150928800-150953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:150932600-150946200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:150935400-150946200	Weak transcription	Aorta	Aorta
6	chr3:150938600-150948600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:150941600-150948000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:150942000-150946800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:150942200-150947000	Enhancers	Primary T cells from cord blood	blood
10	chr3:150942200-150948600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:150942800-150946600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr3:150942800-150947000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:150943000-150946800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:150943000-150947800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:150943200-150946600	Enhancers	Fetal Thymus	thymus
16	chr3:150943200-150948600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:150943600-150946600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:150943600-150946600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr3:150943800-150946400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:150943800-150946600	Enhancers	NHDF-Ad	bronchial
21	chr3:150943800-150946800	Enhancers	Fetal Lung	lung
22	chr3:150943800-150946800	Enhancers	HMEC	breast
23	chr3:150943800-150947000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:150943800-150947000	Enhancers	NHLF	lung
25	chr3:150943800-150947200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:150943800-150947600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:150944000-150946600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:150944000-150946800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:150944000-150946800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:150944000-150946800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:150944000-150946800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:150944000-150947200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:150944000-150948600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:150944200-150946800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:150944200-150948200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:150944600-150946800	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:150944600-150947000	Enhancers	Colon Smooth Muscle	Colon
38	chr3:150944800-150946600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:150944800-150946800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:150944800-150946800	Enhancers	Rectal Smooth Muscle	rectum
41	chr3:150945000-150946200	Enhancers	Psoas Muscle	Psoas
42	chr3:150945000-150946400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:150945000-150946800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:150945000-150947000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:150945200-150946400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:150945200-150946400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:150945200-150946400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:150945200-150946400	Flanking Active TSS	Hela-S3	cervix
49	chr3:150945200-150946600	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:150945200-150946800	Enhancers	H1 Cell Line	embryonic stem cell

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