Variant report

Variant	rs10223012
Chromosome Location	chr4:79148338-79148339
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	chr4:79143866..79146531-chr4:79146925..79148583,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10008653	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10010118	0.88[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs1017649	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10461146	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11730296	0.91[EUR][1000 genomes]
rs11736213	0.94[EUR][1000 genomes]
rs12500443	0.80[AMR][1000 genomes]
rs12501798	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12502139	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12502685	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12504081	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12506036	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12511360	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12511808	0.81[EUR][1000 genomes]
rs13107378	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13108102	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13117388	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13136648	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13138795	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1378239	0.94[EUR][1000 genomes]
rs1454892	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1454898	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1454899	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1484344	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17455826	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1840391	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1840392	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008786	0.94[EUR][1000 genomes]
rs2124143	0.83[EUR][1000 genomes]
rs2124144	0.90[EUR][1000 genomes]
rs2198635	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28737438	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34321445	0.83[EUR][1000 genomes]
rs34535077	0.91[EUR][1000 genomes]
rs34595864	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35290872	0.89[EUR][1000 genomes]
rs35291597	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35419939	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35683023	0.94[EUR][1000 genomes]
rs35828300	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859923	0.91[EUR][1000 genomes]
rs4859924	0.91[EUR][1000 genomes]
rs58101131	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62309861	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62310017	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62310023	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62310045	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6533565	0.94[EUR][1000 genomes]
rs6533571	0.91[EUR][1000 genomes]
rs6815945	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6833721	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs6854043	0.91[CEU][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs6854207	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6856362	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72657047	0.81[ASN][1000 genomes]
rs7656032	0.89[EUR][1000 genomes]
rs7686297	0.80[EUR][1000 genomes]
rs7696792	0.92[EUR][1000 genomes]
rs7698625	0.84[EUR][1000 genomes]
rs9307359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943821	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs943822	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9762380	0.94[EUR][1000 genomes]
rs9994502	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv999844	chr4:79092549-79165869	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv879503	chr4:79108589-79163162	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10223012	THAP6	cis	parietal	SCAN
rs10223012	PARM1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79141600-79148400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:79144200-79176000	Weak transcription	Psoas Muscle	Psoas
3	chr4:79144600-79148600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:79144600-79149400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:79144600-79149800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:79144600-79150200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:79144600-79179000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:79145000-79150000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:79145400-79148600	Weak transcription	Fetal Heart	heart
10	chr4:79145400-79150000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:79146000-79148400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:79146000-79148600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:79146800-79148600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:79146800-79148800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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