Variant report

Variant	rs1647553
Chromosome Location	chr18:11823394-11823395
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	chr18:11822024..11824929-chr18:11829878..11831566,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10048315	0.85[CHB][hapmap]
rs10048316	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs10468681	0.87[CHD][hapmap]
rs11080534	0.87[CHD][hapmap]
rs12607811	0.82[JPT][hapmap];0.89[TSI][hapmap]
rs12965108	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs12965256	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs1364632	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs1477481	0.90[CHD][hapmap]
rs1613471	0.98[ASN][1000 genomes]
rs1614379	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1617064	0.99[ASN][1000 genomes]
rs1647554	0.99[ASN][1000 genomes]
rs1647555	0.99[ASN][1000 genomes]
rs1647557	0.97[ASN][1000 genomes]
rs1647558	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1647559	0.99[ASN][1000 genomes]
rs1647560	0.99[ASN][1000 genomes]
rs16976671	0.80[CHB][hapmap]
rs16976714	0.86[ASN][1000 genomes]
rs16976735	0.85[TSI][hapmap]
rs16976739	0.82[JPT][hapmap]
rs1786563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1786564	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1786565	0.98[ASN][1000 genomes]
rs1786566	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1786567	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2848452	0.86[ASN][1000 genomes]
rs28510090	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28690612	0.87[ASN][1000 genomes]
rs4239301	0.86[AMR][1000 genomes]
rs62097372	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231090	0.99[ASN][1000 genomes]
rs7240632	0.84[CHB][hapmap]
rs7240684	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs9303748	0.92[CEU][hapmap];0.90[CHD][hapmap];0.86[MEX][hapmap]
rs9303749	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs9946370	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9952489	0.87[ASN][1000 genomes]
rs9955115	0.87[ASN][1000 genomes]
rs9959605	0.87[ASN][1000 genomes]
rs9962277	0.92[CEU][hapmap];0.90[CHD][hapmap]
rs9962861	0.87[ASN][1000 genomes]
rs9962908	0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9963000	0.88[ASN][1000 genomes]
rs9963158	0.87[ASN][1000 genomes]
rs9966733	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1647553	RNMT	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11783400-11829200	Weak transcription	Right Atrium	heart
2	chr18:11808000-11830600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:11820400-11824800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr18:11821200-11826600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:11821600-11823800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:11821800-11823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr18:11821800-11826600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr18:11821800-11828800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:11822000-11823600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:11822800-11832200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:11822800-11836600	Weak transcription	Hela-S3	cervix
12	chr18:11823000-11823600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr18:11823000-11823800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr18:11823000-11824000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr18:11823000-11824000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr18:11823000-11824000	Enhancers	K562	blood
17	chr18:11823200-11824000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr18:11823200-11824000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr18:11823200-11824000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr18:11823200-11824200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr18:11823200-11824200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr18:11823200-11824200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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