Variant report

Variant	rs12582273
Chromosome Location	chr12:51739471-51739472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51737875..51739498-chr12:51745613..51748065,2	K562	blood:
2	chr12:51661897..51665217-chr12:51739188..51742261,4	MCF-7	breast:
3	chr12:51476179..51478300-chr12:51738283..51740167,2	K562	blood:
4	chr12:51734941..51739498-chr12:51744423..51748065,5	K562	blood:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876162	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169795	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169805	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11616158	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12310910	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12829179	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12831721	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17860300	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17860301	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17860343	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3858624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3858627	0.84[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs7133606	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7138439	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7299306	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7299453	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306746	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7959814	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7964134	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9651999	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12582273	LOC57228	cis	multi-tissue	Pritchard
rs12582273	ELA1	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51731800-51750600	Weak transcription	Spleen	Spleen
2	chr12:51734800-51740400	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:51735200-51740000	Weak transcription	Pancreas	Pancrea
4	chr12:51735400-51739600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:51735400-51740200	Weak transcription	NHDF-Ad	bronchial
6	chr12:51735400-51741000	Weak transcription	Placenta	Placenta
7	chr12:51735400-51743000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:51735400-51743000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:51735400-51745400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:51735400-51745400	Weak transcription	Brain Substantia Nigra	brain
11	chr12:51735400-51745800	Weak transcription	Fetal Intestine Small	intestine
12	chr12:51735400-51746800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:51735400-51747400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:51735400-51747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:51735400-51747400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:51735400-51747600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:51735400-51747800	Weak transcription	NHLF	lung
18	chr12:51735400-51750200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:51735400-51750600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:51735400-51750600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:51735400-51756000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:51735600-51746800	Weak transcription	Primary T cells from cord blood	blood
23	chr12:51735600-51750600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:51735600-51761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:51735800-51739600	Weak transcription	A549	lung
26	chr12:51735800-51747400	Weak transcription	Dnd41	blood
27	chr12:51736400-51765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:51736600-51742000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:51737200-51739600	Enhancers	GM12878-XiMat	blood
30	chr12:51739000-51740400	Bivalent Enhancer	Primary B cells from cord blood	blood
31	chr12:51739000-51740400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:51739000-51740800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr12:51739000-51741000	Enhancers	Fetal Thymus	thymus
34	chr12:51739200-51739600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr12:51739200-51739800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:51739200-51739800	Bivalent Enhancer	HepG2	liver
37	chr12:51739200-51740000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:51739200-51740000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:51739200-51740000	Enhancers	K562	blood
40	chr12:51739200-51740200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:51739200-51740400	Enhancers	Thymus	Thymus
42	chr12:51739200-51740600	Enhancers	NH-A	brain
43	chr12:51739400-51739600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:51739400-51740000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr12:51739400-51740000	Enhancers	HSMM	muscle
46	chr12:51739400-51740200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:51739400-51740400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:51739400-51740600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:51739400-51740600	Enhancers	Primary hematopoietic stem cells	blood
50	chr12:51739400-51741000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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