Variant report

Variant	rs1319435
Chromosome Location	chr1:210047618-210047619
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	chr1:210042727..210045204-chr1:210046464..210049067,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1073150	0.87[EUR][1000 genomes]
rs11119358	0.86[EUR][1000 genomes]
rs11803382	0.81[CEU][hapmap]
rs1415543	0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs17015218	0.84[CEU][hapmap]
rs17015226	0.84[CEU][hapmap]
rs17015309	0.84[CEU][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17015330	0.87[EUR][1000 genomes]
rs17015361	0.87[EUR][1000 genomes]
rs170554	0.83[AFR][1000 genomes]
rs17317411	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs17389436	0.83[AFR][1000 genomes]
rs2064163	0.82[EUR][1000 genomes]
rs2205984	0.88[AMR][1000 genomes]
rs2206043	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227212	0.83[AFR][1000 genomes]
rs227213	0.83[AFR][1000 genomes]
rs227220	0.83[AFR][1000 genomes]
rs227222	1.00[ASW][hapmap];0.83[AFR][1000 genomes]
rs2357230	0.87[EUR][1000 genomes]
rs3753518	0.84[CEU][hapmap]
rs4556361	0.84[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs55871867	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57315825	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59435160	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60326345	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61747285	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6540560	0.84[CEU][hapmap]
rs6540563	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6540564	0.87[EUR][1000 genomes]
rs6698154	0.87[EUR][1000 genomes]
rs735693	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511996	0.87[EUR][1000 genomes]
rs7525951	0.84[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs7540237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550857	0.84[CEU][hapmap]
rs7551944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846906	1.00[ASW][hapmap]
rs9430025	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1319435	LAMB3	cis	parietal	SCAN
rs1319435	TRAF3IP3	cis	Whole Blood	GTEx
rs1319435	DYRK3	cis	parietal	SCAN
rs1319435	SYT14	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210038000-210048800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:210041000-210055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:210042400-210047800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:210042600-210049400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:210044000-210048400	Weak transcription	Brain Germinal Matrix	brain
6	chr1:210044000-210048800	Weak transcription	Fetal Brain Male	brain
7	chr1:210044400-210049000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:210044600-210048800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:210044600-210048800	Weak transcription	Brain Substantia Nigra	brain
10	chr1:210044600-210049200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:210045200-210049000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:210045200-210049200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:210045200-210051400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:210045400-210048600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:210045400-210048800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:210046400-210048400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:210046400-210049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:210046600-210048200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:210047000-210049000	Weak transcription	NHDF-Ad	bronchial
20	chr1:210047200-210048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:210047200-210048800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:210047200-210048800	Weak transcription	HSMMtube	muscle
23	chr1:210047200-210048800	Weak transcription	Osteobl	bone
24	chr1:210047200-210049200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:210047400-210048800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:210047400-210048800	Weak transcription	Hela-S3	cervix
27	chr1:210047400-210048800	Weak transcription	NH-A	brain
28	chr1:210047400-210049600	Enhancers	NHEK	skin
29	chr1:210047400-210050200	Weak transcription	HUVEC	blood vessel
30	chr1:210047400-210051200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:210047400-210051200	Enhancers	HMEC	breast
32	chr1:210047400-210052600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr1:210047400-210053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:210047600-210049000	Weak transcription	HSMM	muscle
35	chr1:210047600-210049400	Enhancers	Placenta Amnion	Placenta Amnion

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