Variant report

Variant	rs12054220
Chromosome Location	chr3:136677581-136677582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs11711599	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054219	0.82[LWK][hapmap]
rs12629000	1.00[CHB][hapmap]
rs13095028	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13095034	0.84[ASN][1000 genomes]
rs1406539	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1620455	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654924	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1682339	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16844241	1.00[CHB][hapmap]
rs171519	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs183120	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs183121	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2117008	0.80[ASN][1000 genomes]
rs2344092	0.81[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs361233	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs361234	0.82[ASN][1000 genomes]
rs361235	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs361238	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361240	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361249	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs361253	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678275	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4678447	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs71620537	0.84[ASN][1000 genomes]
rs7610507	1.00[CHB][hapmap]
rs7631541	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7648198	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs835632	0.82[LWK][hapmap]
rs835634	0.82[LWK][hapmap]
rs835636	1.00[CHD][hapmap]
rs835637	1.00[CHD][hapmap]
rs835638	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs835652	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9682783	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs9845460	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9875855	0.84[ASN][1000 genomes]

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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12054220	PPP2R3A	cis	parietal	SCAN
rs12054220	PCCB	cis	parietal	SCAN
rs12054220	PCCB	cis	cerebellum	SCAN
rs12054220	SPSB4	cis	cerebellum	SCAN
rs12054220	IL20RB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136656400-136681400	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:136658600-136679400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:136662800-136678800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:136665200-136680200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:136665400-136679000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:136665400-136680200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:136665400-136680200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:136665600-136680000	Weak transcription	Dnd41	blood
9	chr3:136665600-136689400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:136666600-136680400	Weak transcription	Left Ventricle	heart
11	chr3:136669400-136680200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:136673800-136680400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:136674000-136680200	Weak transcription	Fetal Thymus	thymus
14	chr3:136674200-136679800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:136674200-136680200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:136674400-136677600	Weak transcription	Thymus	Thymus
17	chr3:136674600-136680000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:136674800-136680200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:136675000-136679800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:136675400-136677800	Weak transcription	NH-A	brain
21	chr3:136675600-136677600	Weak transcription	Esophagus	oesophagus
22	chr3:136675600-136678200	Enhancers	A549	lung
23	chr3:136675600-136679400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:136675600-136679600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:136675600-136679800	Weak transcription	Osteobl	bone
26	chr3:136675600-136681200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:136675800-136679600	Weak transcription	HSMM	muscle
28	chr3:136676000-136678600	Weak transcription	Small Intestine	intestine
29	chr3:136676200-136679600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:136676200-136680200	Weak transcription	HepG2	liver
31	chr3:136676400-136677800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr3:136676400-136679400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:136676600-136677800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:136676600-136678200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:136676800-136678000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:136677000-136679400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:136677000-136679600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:136677000-136679600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:136677000-136679800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:136677000-136679800	Weak transcription	NHLF	lung
41	chr3:136677200-136677600	Active TSS	K562	blood
42	chr3:136677200-136678800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:136677200-136679400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:136677200-136679600	Transcr. at gene 5' and 3'	NHEK	skin
45	chr3:136677200-136680600	Enhancers	NHDF-Ad	bronchial
46	chr3:136677400-136677600	Active TSS	Hela-S3	cervix
47	chr3:136677400-136678800	Transcr. at gene 5' and 3'	HMEC	breast
48	chr3:136677400-136679400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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