Variant report

Variant	rs7984156
Chromosome Location	chr13:80374537-80374538
allele	C/T
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	TCF12	chr13:80372857-80374607	SK-N-SH	brain:	n/a	n/a
2	EP300	chr13:80371498-80375106	SK-N-SH	brain:	n/a	chr13:80374702-80374716

Variant related genes	Relation type
LINC01038	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10507900	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11619959	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12019641	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428029	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12867107	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1335288	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2039554	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2039555	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2039556	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2152226	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248413	0.84[EUR][1000 genomes]
rs2248563	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2262460	0.85[EUR][1000 genomes]
rs2329137	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2329138	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2783085	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2802638	0.86[EUR][1000 genomes]
rs2802640	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2802641	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35661635	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4885658	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885660	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885669	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4885670	0.82[ASN][1000 genomes]
rs7322877	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7327527	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs915260	0.82[EUR][1000 genomes]
rs9530958	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9530959	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9545191	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9545203	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9545205	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7984156	HIST1H2AM	trans	cerebellum	SCAN

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	chr13:80373600-80377000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:80373600-80377000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:80373600-80377400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:80373600-80378000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:80373600-80378000	Weak transcription	Fetal Muscle Leg	muscle
7	chr13:80373800-80377000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:80373800-80377600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr13:80373800-80378000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:80373800-80378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:80373800-80378200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr13:80373800-80379400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:80374200-80379600	Weak transcription	HSMMtube	muscle
14	chr13:80374200-80384000	Weak transcription	Fetal Heart	heart

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