Variant report

Variant	rs845455
Chromosome Location	chr1:210439367-210439368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10489385	1.00[ASW][hapmap]
rs10489391	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10863818	0.88[EUR][1000 genomes]
rs11119455	0.88[EUR][1000 genomes]
rs11119456	0.81[EUR][1000 genomes]
rs12030512	0.83[AFR][1000 genomes]
rs12030856	0.83[AFR][1000 genomes]
rs12034871	0.83[AFR][1000 genomes]
rs12040684	0.83[AFR][1000 genomes]
rs127043	0.81[EUR][1000 genomes]
rs1774107	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4844987	0.88[EUR][1000 genomes]
rs4844989	0.83[AFR][1000 genomes]
rs4844996	0.83[AFR][1000 genomes]
rs587203	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs588197	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs590380	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs60154123	0.83[AFR][1000 genomes]
rs608791	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs614167	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs628908	0.81[CEU][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs634601	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs646512	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs650728	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661190	0.81[EUR][1000 genomes]
rs662424	0.81[EUR][1000 genomes]
rs664072	0.83[EUR][1000 genomes]
rs664097	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs672819	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689248	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs701941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701942	0.80[CEU][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs701943	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs701944	1.00[ASW][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs815358	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs845452	1.00[ASW][hapmap];0.84[TSI][hapmap];0.83[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	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
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv945274	chr1:210438114-210440537	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs845455	SLC30A1	cis	cerebellum	SCAN
rs845455	CR1	cis	parietal	SCAN
rs845455	SYT14	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210428200-210439600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:210430800-210439600	Enhancers	Fetal Muscle Leg	muscle
3	chr1:210433600-210439400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:210433800-210440200	Enhancers	NHDF-Ad	bronchial
5	chr1:210433800-210445400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:210434400-210439600	Enhancers	Colon Smooth Muscle	Colon
7	chr1:210436400-210445800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:210436600-210439400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:210436600-210439400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:210436600-210439400	Enhancers	Osteobl	bone
11	chr1:210436800-210439600	Enhancers	Stomach Smooth Muscle	stomach
12	chr1:210437200-210439600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:210437200-210439600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:210437600-210439600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:210437800-210440200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:210437800-210440400	Enhancers	Placenta	Placenta
17	chr1:210438000-210439600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:210438000-210439600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:210438200-210439400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr1:210438200-210439600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:210438400-210439400	Enhancers	HepG2	liver
22	chr1:210438600-210443600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:210438800-210439600	Enhancers	Fetal Heart	heart
24	chr1:210439000-210443600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:210439000-210445200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:210439200-210439400	Enhancers	HMEC	breast
27	chr1:210439200-210439600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:210439200-210443200	Weak transcription	NH-A	brain

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