Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52860319..52862626-chr8:52865523..52867110,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC090186.1-6	chr8:52860662-52862694	NONHSAT126544

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12541846	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12543540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12544903	1.00[ASN][1000 genomes]
rs12545812	0.93[ASN][1000 genomes]
rs12545881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2138297	0.90[AFR][1000 genomes]
rs2176119	0.90[AFR][1000 genomes]
rs28451175	1.00[ASN][1000 genomes]
rs56117807	0.97[ASN][1000 genomes]
rs6473665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6982992	1.00[JPT][hapmap]
rs6993171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7015360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73583651	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73583663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7819631	1.00[ASN][1000 genomes]
rs7833668	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs7834181	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs7838307	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs9643465	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11551686	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52831800-52863400	Weak transcription	Aorta	Aorta
2	chr8:52850200-52868000	Weak transcription	Primary B cells from cord blood	blood
3	chr8:52852000-52870000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr8:52852200-52866000	Weak transcription	Left Ventricle	heart
5	chr8:52852600-52862400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr8:52852600-52867600	Weak transcription	Fetal Kidney	kidney
7	chr8:52852800-52867000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:52856800-52865200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:52859600-52863800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:52859800-52866600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr8:52860200-52861200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:52860200-52861200	Enhancers	Fetal Muscle Leg	muscle
13	chr8:52860400-52864400	Weak transcription	Pancreas	Pancrea
14	chr8:52860600-52861200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr8:52860800-52861200	Enhancers	Ovary	ovary
16	chr8:52861000-52861200	ZNF genes & repeats	Adipose Nuclei	Adipose

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