Variant report

Variant	rs9429826
Chromosome Location	chr1:210052146-210052147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210051709..210053987-chr1:210055689..210058098,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10863793	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1108628	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119357	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12022221	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883331	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1963685	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1964106	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2049999	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2142907	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2357231	0.88[CEU][hapmap];0.80[ASN][1000 genomes]
rs4133950	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4308980	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537070	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7537294	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540534	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7542091	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7548545	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550330	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550733	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429825	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9429826	SYT14	cis	Nerve Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210041000-210055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:210047400-210052600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:210047400-210053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:210049400-210052400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:210049400-210052400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:210049400-210052800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:210049400-210052800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:210049400-210056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:210049800-210052200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:210049800-210052200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:210049800-210052200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:210049800-210052600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:210049800-210052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:210050000-210052400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:210050000-210052800	Weak transcription	Osteobl	bone
16	chr1:210050200-210052400	Weak transcription	NH-A	brain
17	chr1:210050200-210052600	Weak transcription	HSMM	muscle
18	chr1:210050200-210052800	Weak transcription	Fetal Brain Female	brain
19	chr1:210050400-210052800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:210050600-210052200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:210050600-210052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:210050600-210052600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:210050800-210052400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:210050800-210052800	Weak transcription	HSMMtube	muscle
25	chr1:210051000-210052600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:210051000-210057400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:210051200-210052200	Weak transcription	NHEK	skin
28	chr1:210051200-210052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:210051200-210052400	Weak transcription	HMEC	breast
30	chr1:210051200-210056200	Weak transcription	NHDF-Ad	bronchial
31	chr1:210051400-210052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:210051800-210052200	Weak transcription	Hela-S3	cervix
33	chr1:210052000-210052600	Enhancers	Brain Hippocampus Middle	brain
34	chr1:210052000-210055600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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