Variant report

Variant	rs3858867
Chromosome Location	chr13:40155612-40155613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40154532..40156238-chr13:40163424..40165796,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1022808	0.84[MEX][hapmap];0.84[TSI][hapmap]
rs1072605	0.82[EUR][1000 genomes]
rs1160321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885758	0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2324344	0.80[CEU][hapmap]
rs2324345	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs2324346	0.81[CEU][hapmap]
rs2324347	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2324349	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4142372	0.81[CEU][hapmap]
rs4456374	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4567589	0.81[CEU][hapmap]
rs4941935	0.86[AMR][1000 genomes]
rs4943674	0.88[AMR][1000 genomes]
rs61956469	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6563720	1.00[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs6563726	0.88[AMR][1000 genomes]
rs6563727	0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6563728	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319551	0.81[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7324883	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7331023	0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7338428	0.88[AMR][1000 genomes]
rs7985507	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7988729	0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs912050	0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs927515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315704	1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9548807	0.88[AMR][1000 genomes]
rs9548835	0.81[CEU][hapmap]
rs9566448	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs9566462	0.81[CEU][hapmap]
rs9576865	0.89[TSI][hapmap]
rs9576869	0.81[CEU][hapmap]
rs978135	0.88[AMR][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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3858867	ALG5	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40139200-40158000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:40140000-40169400	Weak transcription	Fetal Stomach	stomach
3	chr13:40140400-40157800	Weak transcription	Adipose Nuclei	Adipose
4	chr13:40140800-40165400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:40142000-40156200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:40142000-40156200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:40142000-40169400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:40142000-40169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:40143000-40158200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr13:40143200-40157800	Weak transcription	NHDF-Ad	bronchial
11	chr13:40143200-40161800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr13:40143200-40170800	Weak transcription	Osteobl	bone
13	chr13:40146000-40171800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:40146200-40161400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:40147000-40162200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:40150000-40172600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr13:40150400-40170600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr13:40150600-40171800	Weak transcription	HSMM	muscle
19	chr13:40153000-40171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr13:40153200-40156600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr13:40153200-40159800	Enhancers	Fetal Heart	heart
22	chr13:40153200-40171800	Weak transcription	HMEC	breast
23	chr13:40153400-40161000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:40153400-40161400	Weak transcription	Lung	lung
25	chr13:40153400-40161400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:40153600-40155800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr13:40153600-40156200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:40153600-40156200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:40153600-40156200	Weak transcription	Left Ventricle	heart
30	chr13:40153600-40156200	Weak transcription	Right Atrium	heart
31	chr13:40153600-40157800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:40153600-40157800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:40153600-40157800	Weak transcription	Ovary	ovary
34	chr13:40153600-40158000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr13:40153600-40162200	Weak transcription	Psoas Muscle	Psoas
36	chr13:40153600-40170600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:40153600-40171800	Weak transcription	Aorta	Aorta
38	chr13:40154800-40155800	Enhancers	Brain Hippocampus Middle	brain
39	chr13:40154800-40156400	Enhancers	Brain Substantia Nigra	brain
40	chr13:40155000-40156200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:40155000-40156600	Enhancers	Right Ventricle	heart
42	chr13:40155400-40157800	Weak transcription	NHLF	lung
43	chr13:40155600-40156000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:40155600-40156000	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:40155600-40157600	Weak transcription	Brain Angular Gyrus	brain
46	chr13:40155600-40157800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:40155600-40158000	Weak transcription	Colon Smooth Muscle	Colon
48	chr13:40155600-40158800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr13:40155600-40159400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:40155600-40162000	Weak transcription	Fetal Lung	lung

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