Variant report

Variant	rs10778292
Chromosome Location	chr12:104260287-104260288
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	chr12:104235153..104237765-chr12:104259469..104261193,2	K562	blood:
2	chr12:104234662..104237324-chr12:104259230..104262191,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10745984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10861143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10861146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11111815	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111821	0.86[EUR][1000 genomes]
rs11111831	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12302488	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369947	0.91[CEU][hapmap]
rs12371102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034938	0.91[CEU][hapmap]
rs2576969	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3812801	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135138	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6539103	0.95[ASN][1000 genomes]
rs7302036	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968124	0.95[ASN][1000 genomes]
rs7971317	0.95[ASN][1000 genomes]
rs7971563	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9989004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10778292	HSP90B1	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104250000-104263800	Weak transcription	Liver	Liver
2	chr12:104253600-104261600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104254800-104278200	Weak transcription	Aorta	Aorta
4	chr12:104255600-104262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:104257800-104260400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:104258000-104261800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:104259000-104260400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:104259200-104261400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:104259200-104261400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:104259200-104262400	Weak transcription	HSMM	muscle
11	chr12:104259200-104263800	Weak transcription	HepG2	liver
12	chr12:104259600-104261400	Weak transcription	HSMMtube	muscle
13	chr12:104260200-104262800	Enhancers	Colon Smooth Muscle	Colon

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