Variant report

Variant	rs12513356
Chromosome Location	chr4:151152940-151152941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151151694..151154346-chr4:151156104..151158650,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12501888	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506758	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12512965	1.00[GIH][hapmap]
rs1504782	1.00[GIH][hapmap]
rs4240358	0.81[JPT][hapmap]
rs4835621	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs58654970	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72617457	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7679888	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7692551	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12513356	LAYN	trans	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151114200-151154200	Weak transcription	Aorta	Aorta
2	chr4:151130600-151156000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:151138800-151153200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:151138800-151153400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:151138800-151153400	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:151138800-151169800	Weak transcription	Spleen	Spleen
7	chr4:151139000-151153600	Weak transcription	Adipose Nuclei	Adipose
8	chr4:151139600-151177400	Weak transcription	Brain Substantia Nigra	brain
9	chr4:151139600-151181000	Weak transcription	Brain Angular Gyrus	brain
10	chr4:151139800-151153200	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:151139800-151153600	Weak transcription	Brain Anterior Caudate	brain
12	chr4:151140000-151175000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:151141400-151153800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:151142200-151172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:151145800-151153800	Enhancers	Fetal Heart	heart
16	chr4:151146200-151169200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:151146400-151157400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:151146400-151157400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:151146400-151165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:151146600-151153400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:151146600-151156400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:151146600-151165600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:151147000-151153800	Enhancers	Brain Germinal Matrix	brain
24	chr4:151147200-151153000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:151148600-151153800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:151149800-151153600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:151149800-151153600	Weak transcription	HSMMtube	muscle
28	chr4:151150000-151153600	Enhancers	Fetal Brain Male	brain
29	chr4:151150200-151153200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:151150400-151153000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:151150400-151153400	Enhancers	Osteobl	bone
32	chr4:151150400-151153600	Enhancers	Fetal Brain Female	brain
33	chr4:151150400-151153600	Enhancers	Fetal Lung	lung
34	chr4:151150400-151153800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:151150400-151153800	Enhancers	NH-A	brain
36	chr4:151150400-151153800	Enhancers	NHLF	lung
37	chr4:151150400-151154000	Enhancers	HUVEC	blood vessel
38	chr4:151150800-151153000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:151150800-151153000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:151150800-151153200	Weak transcription	Left Ventricle	heart
41	chr4:151150800-151153200	Weak transcription	Right Atrium	heart
42	chr4:151150800-151153600	Weak transcription	Ovary	ovary
43	chr4:151150800-151153600	Weak transcription	HSMM	muscle
44	chr4:151150800-151155000	Weak transcription	Right Ventricle	heart
45	chr4:151150800-151156800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:151150800-151156800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:151150800-151157800	Weak transcription	Fetal Kidney	kidney
48	chr4:151150800-151170800	Weak transcription	Pancreas	Pancrea
49	chr4:151151000-151155800	Weak transcription	Fetal Stomach	stomach
50	chr4:151151400-151153400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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