Variant report

Variant	rs12865501
Chromosome Location	chr13:40395013-40395014
allele	C/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	RAD21	chr13:40394754-40395141	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr13:40394770-40395041	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr13:40394780-40395143	H1-hESC	embryonic stem cell:	n/a	n/a
4	TEAD4	chr13:40394744-40395168	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr13:40394815-40395245	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr13:40394880-40395030	HRPEpiC	eye:	n/a	n/a
7	GATA2	chr13:40394649-40395107	SH-SY5Y	brain:	n/a	chr13:40394810-40394827

Variant related genes	Relation type
CDKN2AIPNLP3	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1555629	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2209234	0.81[ASN][1000 genomes]
rs2324458	0.81[EUR][1000 genomes]
rs35023159	0.92[ASN][1000 genomes]
rs4379951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432144	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4447298	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4556674	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4575406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943703	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943705	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61955567	0.92[ASN][1000 genomes]
rs6563756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563757	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563758	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563764	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563765	0.93[ASN][1000 genomes]
rs6563766	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563768	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7323371	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7325743	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336265	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997407	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285137	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532443	0.88[ASN][1000 genomes]
rs9548943	0.88[ASN][1000 genomes]
rs9548944	0.96[ASN][1000 genomes]
rs9548945	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576905	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576907	0.81[ASN][1000 genomes]
rs9594373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9603628	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40382600-40404000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:40392200-40395800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:40392400-40408600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:40392600-40396000	Weak transcription	Ovary	ovary
5	chr13:40394800-40395200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:40394800-40395400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:40395000-40395200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:40395000-40395200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:40395000-40395200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr13:40395000-40395400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr13:40395000-40397600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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