Variant report

Variant	rs1678778
Chromosome Location	chr1:93502451-93502452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93477075..93479957-chr1:93501163..93503966,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11164860	0.88[ASN][1000 genomes]
rs11164861	0.86[ASN][1000 genomes]
rs12022729	0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12023767	0.85[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs12027025	0.96[ASN][1000 genomes]
rs12039256	0.96[ASN][1000 genomes]
rs12043577	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12119421	0.94[ASN][1000 genomes]
rs12130551	0.86[ASN][1000 genomes]
rs12134501	0.96[ASN][1000 genomes]
rs12141895	0.96[ASN][1000 genomes]
rs2086312	0.86[ASN][1000 genomes]
rs2253595	0.96[ASN][1000 genomes]
rs2492898	0.95[ASN][1000 genomes]
rs2815417	0.84[JPT][hapmap]
rs2928183	0.87[ASN][1000 genomes]
rs4626900	0.94[ASN][1000 genomes]
rs4847227	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs485336	0.96[ASN][1000 genomes]
rs486370	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs492054	0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs492754	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs496465	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs497540	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs504418	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517856	0.93[ASN][1000 genomes]
rs521527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524045	0.95[ASN][1000 genomes]
rs544285	0.84[JPT][hapmap]
rs553396	0.88[ASN][1000 genomes]
rs557812	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56320266	0.85[ASN][1000 genomes]
rs572131	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs57478994	0.95[ASN][1000 genomes]
rs590296	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591820	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs591868	0.89[ASN][1000 genomes]
rs592751	0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs664524	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664852	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674738	0.85[ASN][1000 genomes]
rs680285	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs808833	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9787147	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1678778	BCAR3	cis	lymphoblastoid	seeQTL
rs1678778	MTF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93488000-93504200	Enhancers	Fetal Thymus	thymus
2	chr1:93495800-93504200	Weak transcription	Primary T cells from cord blood	blood
3	chr1:93496800-93503600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:93499400-93505000	Enhancers	Dnd41	blood
5	chr1:93499800-93507800	Weak transcription	K562	blood
6	chr1:93500200-93503600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:93500400-93503800	Weak transcription	GM12878-XiMat	blood
8	chr1:93500400-93507800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:93501400-93502600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:93501600-93507600	Weak transcription	Thymus	Thymus
11	chr1:93502400-93506600	Weak transcription	HepG2	liver

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