Variant report

Variant	rs380650
Chromosome Location	chr7:138012161-138012162
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138011680..138013976-chr7:138143884..138146522,2	K562	blood:

Variant related genes	Relation type
ENSG00000122779	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11983566	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643164	0.91[ASN][1000 genomes]
rs357371	0.88[ASN][1000 genomes]
rs357372	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs357381	0.94[ASN][1000 genomes]
rs357382	0.92[ASN][1000 genomes]
rs357383	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs357386	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs357404	0.82[AMR][1000 genomes]
rs357411	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs357412	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs357414	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs357421	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs357427	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs357428	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs357435	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs357437	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs357445	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs357451	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs357454	0.93[ASN][1000 genomes]
rs357456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs357457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs367783	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs370275	0.88[ASN][1000 genomes]
rs373613	0.94[ASN][1000 genomes]
rs375018	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs382122	0.91[ASN][1000 genomes]
rs385127	0.90[ASN][1000 genomes]
rs392162	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs396918	0.89[ASN][1000 genomes]
rs397203	0.90[ASN][1000 genomes]
rs398970	0.91[ASN][1000 genomes]
rs399486	0.91[ASN][1000 genomes]
rs402228	0.91[ASN][1000 genomes]
rs402358	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs402486	0.93[ASN][1000 genomes]
rs407687	0.89[ASN][1000 genomes]
rs409813	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs424605	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427954	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs428488	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs429103	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431358	0.91[ASN][1000 genomes]
rs432187	0.91[ASN][1000 genomes]
rs446384	0.92[ASN][1000 genomes]
rs447273	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs449239	0.94[ASN][1000 genomes]
rs60969	0.84[CHB][hapmap];0.91[ASN][1000 genomes]
rs689683	0.91[ASN][1000 genomes]
rs690193	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831152	chr7:137884311-138033117	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv5967	chr7:137988239-138015844	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs380650	BRAF	cis	cerebellum	SCAN
rs380650	CLEC5A	cis	cerebellum	SCAN
rs380650	ACOT2	trans	lymphoblastoid	seeQTL
rs380650	DGKI	cis	lymphoblastoid	seeQTL
rs380650	AKR1B10	cis	parietal	SCAN
rs380650	RNF219	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138006200-138012400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:138010000-138012400	Weak transcription	Fetal Heart	heart
3	chr7:138010000-138012400	Weak transcription	Placenta	Placenta
4	chr7:138010400-138012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:138011400-138013600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:138012000-138013200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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