Variant report

Variant	rs55945889
Chromosome Location	chr12:48572158-48572159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48569957..48573539-chr12:48589775..48593231,3	K562	blood:
2	chr12:48570309..48573490-chr12:48574476..48577438,4	MCF-7	breast:
3	chr12:48570659..48574858-chr12:48591622..48593711,4	K562	blood:
4	chr12:48570737..48572645-chr12:48574965..48576517,2	K562	blood:

Variant related genes	Relation type
ENSG00000177875	Chromatin interaction
ENSG00000269514	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1004746	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1004806	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10506276	0.84[EUR][1000 genomes]
rs10506277	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11830378	0.84[EUR][1000 genomes]
rs17122802	0.84[EUR][1000 genomes]
rs17224674	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17224828	0.84[EUR][1000 genomes]
rs17225261	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17225366	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17225751	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17607800	0.87[AFR][1000 genomes]
rs17823193	0.84[EUR][1000 genomes]
rs17824200	0.89[AMR][1000 genomes]
rs2228501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3936179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4075914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41291959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41291961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55682541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55707383	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55752728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55794326	0.89[AMR][1000 genomes]
rs55886138	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55890195	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55894137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55953382	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56049209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56116946	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56187356	1.00[EUR][1000 genomes]
rs56205628	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56288528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56378908	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73304917	0.86[EUR][1000 genomes]
rs74089155	1.00[EUR][1000 genomes]
rs74089159	0.88[EUR][1000 genomes]
rs74089163	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active 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	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55945889	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48570000-48573200	Weak transcription	Fetal Kidney	kidney
2	chr12:48570200-48575200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:48570600-48575000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:48571200-48572400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:48571200-48576200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48571400-48573000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:48571400-48576000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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