Variant report

Variant	rs2064163
Chromosome Location	chr1:210048819-210048820
allele	G/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:
2	chr1:210033344..210033878-chr1:210048801..210049436,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1044516	0.83[TSI][hapmap]
rs11119358	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12062600	0.80[ASN][1000 genomes]
rs12063989	0.80[ASN][1000 genomes]
rs12064085	0.80[ASN][1000 genomes]
rs12064211	0.80[ASN][1000 genomes]
rs12066340	0.80[ASN][1000 genomes]
rs12078157	0.80[ASN][1000 genomes]
rs1319435	0.82[EUR][1000 genomes]
rs17015218	0.83[TSI][hapmap]
rs17015226	0.83[TSI][hapmap]
rs17015259	0.84[CEU][hapmap]
rs2073485	0.83[TSI][hapmap]
rs2206043	0.83[EUR][1000 genomes]
rs2235372	0.83[TSI][hapmap]
rs4844895	0.83[TSI][hapmap]
rs57315825	0.86[EUR][1000 genomes]
rs59435160	0.86[EUR][1000 genomes]
rs60326345	0.86[EUR][1000 genomes]
rs6540560	0.82[TSI][hapmap]
rs6696825	0.85[MEX][hapmap]
rs735693	0.86[EUR][1000 genomes]
rs735694	0.81[EUR][1000 genomes]
rs742215	0.83[TSI][hapmap]
rs7540237	0.82[EUR][1000 genomes]
rs7550857	0.83[TSI][hapmap]
rs7551944	0.81[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2064163	SYT14	cis	parietal	SCAN
rs2064163	LPGAT1	cis	cerebellum	SCAN
rs2064163	TRAF3IP3	cis	Whole Blood	GTEx
rs2064163	LAMB3	cis	parietal	SCAN
rs2064163	IRF6	cis	cerebellum	SCAN

Chromatin state (count:45 , 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	chr1:210042600-210049400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:210044400-210049000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:210044600-210049200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:210045200-210049000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:210045200-210049200	Weak transcription	Brain Angular Gyrus	brain
7	chr1:210045200-210051400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:210046400-210049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:210047000-210049000	Weak transcription	NHDF-Ad	bronchial
10	chr1:210047200-210049200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:210047400-210049600	Enhancers	NHEK	skin
12	chr1:210047400-210050200	Weak transcription	HUVEC	blood vessel
13	chr1:210047400-210051200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:210047400-210051200	Enhancers	HMEC	breast
15	chr1:210047400-210052600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:210047400-210053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:210047600-210049000	Weak transcription	HSMM	muscle
18	chr1:210047600-210049400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:210048400-210049000	Enhancers	Brain Germinal Matrix	brain
20	chr1:210048400-210049800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:210048600-210049000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:210048600-210049000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:210048600-210049400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr1:210048800-210049000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:210048800-210049000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:210048800-210049000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr1:210048800-210049000	Enhancers	Brain Substantia Nigra	brain
28	chr1:210048800-210049000	Enhancers	NH-A	brain
29	chr1:210048800-210049000	Flanking Active TSS	Osteobl	bone
30	chr1:210048800-210049400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:210048800-210049400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:210048800-210049400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:210048800-210049400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:210048800-210049400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:210048800-210049400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:210048800-210049400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:210048800-210049400	Enhancers	Ovary	ovary
38	chr1:210048800-210049600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr1:210048800-210049600	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr1:210048800-210049800	Enhancers	NHLF	lung
41	chr1:210048800-210050600	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:210048800-210050600	Enhancers	Fetal Brain Male	brain
43	chr1:210048800-210050800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:210048800-210050800	Enhancers	HSMMtube	muscle
45	chr1:210048800-210051800	Enhancers	Hela-S3	cervix

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