Variant report

Variant	rs12561944
Chromosome Location	chr1:70910065-70910066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70905812-70910297	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000271992	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12561855	0.84[ASN][1000 genomes]
rs12562375	0.86[ASN][1000 genomes]
rs12562432	0.84[ASN][1000 genomes]
rs12562754	0.84[ASN][1000 genomes]
rs12565977	0.83[ASN][1000 genomes]
rs3806385	0.90[CEU][hapmap]
rs45615634	0.81[AMR][1000 genomes]
rs55952366	0.82[ASN][1000 genomes]
rs57174209	0.94[ASN][1000 genomes]
rs57922519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60589571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61704484	0.95[ASN][1000 genomes]
rs6413472	0.91[CEU][hapmap]
rs6667807	0.85[ASN][1000 genomes]
rs74085262	0.85[ASN][1000 genomes]
rs74085263	0.86[ASN][1000 genomes]
rs74085264	0.84[ASN][1000 genomes]
rs74085265	0.83[ASN][1000 genomes]
rs74085266	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12561944	CTH	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70895800-70912000	Weak transcription	Hela-S3	cervix
2	chr1:70900200-70913800	Weak transcription	Dnd41	blood
3	chr1:70900200-70914800	Weak transcription	K562	blood
4	chr1:70904600-70915000	Weak transcription	Aorta	Aorta
5	chr1:70906400-70910400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:70906800-70910200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:70907000-70910200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:70907000-70914000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:70907200-70910200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:70907400-70910200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:70908400-70912800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:70908400-70915000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:70908400-70918600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:70908600-70910200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:70908600-70914400	Weak transcription	Liver	Liver
16	chr1:70909000-70928200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:70909200-70910200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:70909200-70913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:70909400-70910200	Enhancers	Brain Germinal Matrix	brain
20	chr1:70910000-70910200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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