Variant report

Variant	rs1998073
Chromosome Location	chr6:132557000-132557001
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:132269655-132282174..6:132556576-132559814	GM12878	blood:
2	6:132182612-132191683..6:132556576-132559814	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000227220	Chromatin interaction
ENSG00000118523	Chromatin interaction
ENSG00000197594	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10456995	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10457585	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11154668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12212796	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1406936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998074	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998075	0.86[CEU][hapmap];0.86[CHD][hapmap];0.93[MEX][hapmap]
rs6902875	0.80[EUR][1000 genomes]
rs6906965	0.86[CEU][hapmap];0.85[AMR][1000 genomes]
rs6911439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925688	0.80[EUR][1000 genomes]
rs7738705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752092	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756650	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs7758221	0.81[CEU][hapmap]
rs7771572	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7772637	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321333	1.00[CEU][hapmap];0.88[JPT][hapmap];0.99[EUR][1000 genomes]
rs9321334	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs9402393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402395	0.99[EUR][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	esv2762616	chr6:132404708-132584324	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1024527	chr6:132532941-132571889	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1998073	BCLAF1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132550800-132557000	Weak transcription	NH-A	brain
2	chr6:132552200-132562400	Weak transcription	Psoas Muscle	Psoas
3	chr6:132553000-132557600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:132553800-132557800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:132555600-132558200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:132555600-132558400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:132555800-132557600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:132556000-132557000	Weak transcription	HSMM	muscle
9	chr6:132556000-132557200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:132556200-132557200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:132556200-132558000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:132556400-132557000	Enhancers	Rectal Smooth Muscle	rectum
13	chr6:132556400-132558600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:132556600-132557400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:132556600-132557400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:132556600-132557800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:132556600-132558000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:132556600-132558200	Enhancers	NHLF	lung
19	chr6:132556600-132558200	Enhancers	Osteobl	bone
20	chr6:132556800-132557200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:132556800-132558200	Enhancers	HMEC	breast
22	chr6:132556800-132558200	Enhancers	HSMMtube	muscle
23	chr6:132556800-132558400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:132557000-132558000	Enhancers	HSMM	muscle
25	chr6:132557000-132558200	Enhancers	NH-A	brain
26	chr6:132557000-132558400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:132557000-132558800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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