Variant report

Variant	rs1560844
Chromosome Location	chr18:39210461-39210462
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10163854	0.89[EUR][1000 genomes]
rs10221329	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10502770	0.95[EUR][1000 genomes]
rs10502771	0.98[EUR][1000 genomes]
rs10502772	0.90[EUR][1000 genomes]
rs11875076	0.88[EUR][1000 genomes]
rs13381575	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1368833	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1433929	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16975000	0.96[EUR][1000 genomes]
rs16975004	0.96[EUR][1000 genomes]
rs16975007	0.96[EUR][1000 genomes]
rs16975010	0.95[EUR][1000 genomes]
rs16975012	0.96[EUR][1000 genomes]
rs16975017	0.96[EUR][1000 genomes]
rs16975021	0.95[EUR][1000 genomes]
rs16975022	0.95[EUR][1000 genomes]
rs16975025	0.95[EUR][1000 genomes]
rs16975035	0.82[EUR][1000 genomes]
rs16975049	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16975051	0.84[EUR][1000 genomes]
rs1942063	0.98[EUR][1000 genomes]
rs1942065	0.99[EUR][1000 genomes]
rs1942069	0.95[EUR][1000 genomes]
rs1942070	0.95[EUR][1000 genomes]
rs2156006	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2315174	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28374486	0.92[EUR][1000 genomes]
rs28414473	0.92[EUR][1000 genomes]
rs35462279	0.96[EUR][1000 genomes]
rs4404160	0.89[EUR][1000 genomes]
rs55797333	0.98[EUR][1000 genomes]
rs56812327	0.98[EUR][1000 genomes]
rs57249168	0.98[EUR][1000 genomes]
rs58350157	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507424	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6507425	0.90[EUR][1000 genomes]
rs6507428	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7229356	0.92[EUR][1000 genomes]
rs7237488	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7244165	0.89[EUR][1000 genomes]
rs72905911	0.82[EUR][1000 genomes]
rs72905915	0.90[EUR][1000 genomes]
rs72905919	0.87[EUR][1000 genomes]
rs72905923	0.96[EUR][1000 genomes]
rs72905924	0.96[EUR][1000 genomes]
rs72905927	0.87[EUR][1000 genomes]
rs72905935	0.87[EUR][1000 genomes]
rs72905937	0.87[EUR][1000 genomes]
rs72905948	0.96[EUR][1000 genomes]
rs72905963	0.98[EUR][1000 genomes]
rs72905965	0.98[EUR][1000 genomes]
rs72905967	0.98[EUR][1000 genomes]
rs72905973	0.89[EUR][1000 genomes]
rs72905979	0.98[EUR][1000 genomes]
rs72905981	0.89[EUR][1000 genomes]
rs72905986	0.89[EUR][1000 genomes]
rs72905989	0.89[EUR][1000 genomes]
rs72907804	0.89[EUR][1000 genomes]
rs72907808	0.89[EUR][1000 genomes]
rs72907815	0.89[EUR][1000 genomes]
rs72907817	0.89[EUR][1000 genomes]
rs72907819	0.89[EUR][1000 genomes]
rs72907821	0.89[EUR][1000 genomes]
rs72907830	0.89[EUR][1000 genomes]
rs72907836	0.89[EUR][1000 genomes]
rs72907842	0.89[EUR][1000 genomes]
rs72907845	0.89[EUR][1000 genomes]
rs72907847	0.89[EUR][1000 genomes]
rs72907848	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72907850	0.89[EUR][1000 genomes]
rs72907851	0.89[EUR][1000 genomes]
rs72907854	0.86[EUR][1000 genomes]
rs72907855	0.89[EUR][1000 genomes]
rs72907861	0.90[EUR][1000 genomes]
rs72907862	0.90[EUR][1000 genomes]
rs72909913	0.90[EUR][1000 genomes]
rs72909936	0.90[EUR][1000 genomes]
rs72909959	0.90[EUR][1000 genomes]
rs734357	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73450796	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8087434	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8087485	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8098315	0.89[EUR][1000 genomes]
rs8098394	0.89[EUR][1000 genomes]
rs9304250	0.80[EUR][1000 genomes]
rs9949338	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9956251	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9965809	0.99[EUR][1000 genomes];0.94[ASN][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	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1560844	RP11-142I20.1	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39204800-39211400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:39207000-39211400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:39209800-39212200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:39210000-39211000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr18:39210200-39210600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:39210200-39210600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:39210200-39210600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:39210200-39210800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr18:39210200-39210800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr18:39210200-39210800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:39210200-39211000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr18:39210200-39211000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr18:39210400-39210600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr18:39210400-39210600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr18:39210400-39211400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:39210400-39211600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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