Variant report

Variant	rs2483141
Chromosome Location	chr1:160941743-160941744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12132502	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2039223	0.84[CEU][hapmap];0.92[CHB][hapmap]
rs2184065	0.92[CHB][hapmap];0.99[ASN][1000 genomes]
rs2245672	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246145	0.92[CHB][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246484	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246485	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247472	0.92[CEU][hapmap];0.92[CHB][hapmap]
rs2249409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249933	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250174	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250193	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250304	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256505	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256625	0.92[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265239	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2265242	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2481073	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483139	0.92[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483140	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483142	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2779801	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2988722	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2990694	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007155	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4483427	0.81[ASN][1000 genomes]
rs6427563	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427571	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6677526	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6677533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790055	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap]
rs790056	0.92[CEU][hapmap];0.92[CHB][hapmap]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2483141	TSTD1	cis	Nerve Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160931000-160942000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:160941200-160941800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:160941200-160941800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:160941200-160942200	Enhancers	GM12878-XiMat	blood
5	chr1:160941200-160942600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:160941200-160942800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:160941200-160943200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:160941200-160943800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:160941200-160943800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:160941400-160941800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:160941400-160941800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:160941400-160941800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:160941400-160941800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:160941400-160942000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:160941400-160942000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr1:160941400-160942000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:160941400-160942000	Enhancers	NHEK	skin
18	chr1:160941400-160942200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:160941400-160943800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:160941600-160941800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:160941600-160942000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:160941600-160942000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:160941600-160942800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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