Variant report

Variant	rs12814413
Chromosome Location	chr12:56916614-56916615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56916521..56918137-chr12:56919957..56922129,2	MCF-7	breast:
2	chr12:56916433..56918956-chr12:56923495..56926214,2	MCF-7	breast:
3	chr12:56916195..56918397-chr12:57055172..57057323,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10735863	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783786	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876891	0.96[MEX][hapmap]
rs10876897	0.94[ASN][1000 genomes]
rs10876899	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876902	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876903	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11171883	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11171884	0.80[EUR][1000 genomes]
rs11171887	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11614642	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1965307	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34900037	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34948728	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3782235	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581097	0.80[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581098	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581099	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7131699	0.80[JPT][hapmap]
rs7132918	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7132965	0.89[EUR][1000 genomes]
rs7136456	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7299115	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303549	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7303717	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7305759	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7313637	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313983	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314300	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7975238	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12814413	RBMS2	cis	cerebellum	SCAN
rs12814413	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs12814413	SNORD59A	cis	cerebellum	SCAN
rs12814413	ESYT1	cis	cerebellum	SCAN
rs12814413	RBMS2	cis	multi-tissue	Pritchard
rs12814413	RBMS2	cis	lymphoblastoid	seeQTL
rs12814413	AMHR2	cis	cerebellum	SCAN
rs12814413	OR6C76	cis	parietal	SCAN
rs12814413	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs12814413	ITGA5	cis	cerebellum	SCAN
rs12814413	RBMS2	cis	Whole Blood	GTEx
rs12814413	ATF7	cis	parietal	SCAN
rs12814413	GLI1	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56912800-56917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:56914000-56917000	Active TSS	Aorta	Aorta
3	chr12:56914000-56917400	Active TSS	Right Atrium	heart
4	chr12:56914000-56917400	Active TSS	Right Ventricle	heart
5	chr12:56914000-56918400	Active TSS	Stomach Smooth Muscle	stomach
6	chr12:56914000-56919200	Weak transcription	Spleen	Spleen
7	chr12:56914200-56916800	Active TSS	Duodenum Mucosa	Duodenum
8	chr12:56914200-56917200	Active TSS	Psoas Muscle	Psoas
9	chr12:56914400-56918600	Active TSS	NHLF	lung
10	chr12:56915000-56917000	Active TSS	Ovary	ovary
11	chr12:56915000-56917200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:56915000-56917200	Active TSS	Colonic Mucosa	Colon
13	chr12:56915000-56917200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:56915000-56917600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:56915000-56917600	Active TSS	NHDF-Ad	bronchial
16	chr12:56915000-56918600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:56915000-56918600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr12:56915200-56916800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:56915200-56916800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:56915200-56917000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:56915200-56917000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:56915200-56917000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:56915200-56917000	Active TSS	Left Ventricle	heart
24	chr12:56915200-56917000	Active TSS	Thymus	Thymus
25	chr12:56915200-56917200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:56915200-56917200	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:56915200-56917200	Active TSS	Placenta	Placenta
28	chr12:56915200-56917400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr12:56915200-56917400	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr12:56915200-56917800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:56915200-56918000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:56915200-56918400	Active TSS	HMEC	breast
33	chr12:56915200-56918800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:56915200-56919000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:56915400-56916800	Active TSS	Osteobl	bone
36	chr12:56915400-56917000	Active TSS	HSMMtube	muscle
37	chr12:56915400-56917400	Active TSS	Fetal Stomach	stomach
38	chr12:56915400-56917800	Active TSS	A549	lung
39	chr12:56915400-56917800	Active TSS	Hela-S3	cervix
40	chr12:56915400-56918000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:56915400-56918000	Active TSS	NHEK	skin
42	chr12:56915400-56918200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:56915400-56918200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:56915400-56918400	Active TSS	HSMM	muscle
45	chr12:56915600-56916800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:56915600-56916800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:56915600-56916800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:56915600-56916800	Active TSS	Esophagus	oesophagus
49	chr12:56915600-56917000	Active TSS	H1 Cell Line	embryonic stem cell
50	chr12:56915600-56917800	Active TSS	Muscle Satellite Cultured Cells	--

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