Variant report

Variant	rs9530960
Chromosome Location	chr13:80373908-80373909
allele	A/C
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	GATA3	chr13:80373068-80374181	SH-SY5Y	brain:	n/a	chr13:80373247-80373255
2	POLR2A	chr13:80373076-80374071	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr13:80372853-80374351	SK-N-SH	brain:	n/a	chr13:80373247-80373255
4	TCF12	chr13:80372857-80374607	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr13:80372906-80374328	SK-N-SH	brain:	n/a	n/a
6	MAX	chr13:80373281-80373965	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr13:80373023-80374200	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr13:80373029-80374203	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr13:80373090-80374183	SH-SY5Y	brain:	n/a	chr13:80373247-80373255
10	EP300	chr13:80371498-80375106	SK-N-SH	brain:	n/a	chr13:80374702-80374716
11	MAX	chr13:80373630-80374018	SK-N-SH	brain:	n/a	n/a
12	YY1	chr13:80373582-80373916	SK-N-SH_RA	brain:	n/a	n/a
13	FOXM1	chr13:80373049-80374149	SK-N-SH	brain:	n/a	n/a
14	RAD21	chr13:80373098-80374006	SK-N-SH_RA	brain:	n/a	n/a
15	JUND	chr13:80373018-80374122	SK-N-SH	brain:	n/a	n/a
16	FOXM1	chr13:80372899-80374112	SK-N-SH	brain:	n/a	n/a
17	EP300	chr13:80373046-80374133	SK-N-SH_RA	brain:	n/a	n/a
18	NFIC	chr13:80372982-80374245	SK-N-SH	brain:	n/a	n/a
19	EP300	chr13:80373006-80374178	SK-N-SH_RA	brain:	n/a	n/a
20	EP300	chr13:80372979-80374071	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr13:80373594-80373989	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr13:80373038-80374265	SK-N-SH	brain:	n/a	chr13:80373247-80373255
23	PBX3	chr13:80373028-80374224	SK-N-SH	brain:	n/a	n/a
24	EP300	chr13:80372891-80374230	SK-N-SH	brain:	n/a	n/a
25	JUND	chr13:80373027-80374085	SK-N-SH	brain:	n/a	n/a
26	PBX3	chr13:80373033-80374088	SK-N-SH	brain:	n/a	n/a
27	RAD21	chr13:80373584-80373959	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
LINC01038	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1158596	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1160131	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1414109	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4319636	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7321213	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7324675	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9318656	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9318657	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9545192	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9545193	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9545204	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9574473	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9574484	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9601268	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv900590	chr13:80342186-80421340	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80367800-80377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:80372000-80374200	Enhancers	HSMMtube	muscle
3	chr13:80372600-80374200	Enhancers	Fetal Heart	heart
4	chr13:80373600-80377000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:80373600-80377000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:80373600-80377400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:80373600-80378000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:80373600-80378000	Weak transcription	Fetal Muscle Leg	muscle
9	chr13:80373800-80377000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:80373800-80377600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:80373800-80378000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:80373800-80378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:80373800-80378200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:80373800-80379400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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