Variant report

Variant	rs12831721
Chromosome Location	chr12:51723727-51723728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51712710..51714894-chr12:51720855..51723845,2	K562	blood:
2	chr12:51710356..51713645-chr12:51720668..51723733,3	MCF-7	breast:
3	chr12:51719185..51720763-chr12:51721819..51723856,2	MCF-7	breast:
4	chr12:51662774..51665391-chr12:51722763..51725080,2	MCF-7	breast:
5	chr12:51712710..51716828-chr12:51719754..51724043,5	K562	blood:
6	chr12:51686282..51687950-chr12:51722730..51724837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10516	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs10876162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169795	0.96[CEU][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap]
rs11169805	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11616158	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310910	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12582273	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]
rs12829179	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830766	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17296815	0.86[ASW][hapmap];1.00[LWK][hapmap]
rs17860300	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860301	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17860343	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3858624	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3858627	0.87[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4761998	0.86[ASW][hapmap];1.00[LWK][hapmap]
rs57941347	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61022955	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs68042460	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7133606	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7138439	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7299306	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7299453	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7306746	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7959814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964134	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9651999	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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	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	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12831721	ELA1	cis	multi-tissue	Pritchard
rs12831721	SPATS2	cis	parietal	SCAN
rs12831721	LOC57228	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:51718400-51724400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:51718400-51724400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:51718400-51724400	Enhancers	Placenta	Placenta
6	chr12:51718400-51724400	Enhancers	Fetal Thymus	thymus
7	chr12:51718400-51727800	Weak transcription	Colonic Mucosa	Colon
8	chr12:51719600-51723800	Enhancers	Dnd41	blood
9	chr12:51719800-51724200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:51720800-51728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:51720800-51735000	Weak transcription	Esophagus	oesophagus
12	chr12:51721000-51724200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr12:51721000-51724400	Enhancers	Primary hematopoietic stem cells	blood
14	chr12:51721200-51723800	Weak transcription	HSMMtube	muscle
15	chr12:51721200-51724200	Enhancers	Primary B cells from cord blood	blood
16	chr12:51721200-51724600	Weak transcription	A549	lung
17	chr12:51721200-51735000	Weak transcription	NHDF-Ad	bronchial
18	chr12:51721400-51723800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:51721400-51723800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:51721400-51724400	Enhancers	GM12878-XiMat	blood
21	chr12:51722000-51724200	Enhancers	K562	blood
22	chr12:51722200-51724000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr12:51722400-51724200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr12:51722400-51724200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr12:51722600-51723800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr12:51722600-51724000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:51722600-51735000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:51722800-51723800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr12:51722800-51724000	Weak transcription	Hela-S3	cervix
30	chr12:51723000-51724000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr12:51723000-51724200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:51723000-51724200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:51723200-51723800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr12:51723200-51723800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:51723200-51724200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:51723200-51724200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:51723200-51724400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr12:51723200-51724400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:51723400-51723800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr12:51723400-51724000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:51723400-51724200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:51723400-51724400	Enhancers	Osteobl	bone
43	chr12:51723600-51724000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr12:51723600-51724400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:51723600-51724400	Enhancers	Thymus	Thymus
46	chr12:51723600-51724600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr12:51723600-51725600	Weak transcription	Rectal Mucosa Donor 31	rectum

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