Variant report

Variant	rs9968886
Chromosome Location	chr6:39060478-39060479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38964768..38966045-chr6:39059915..39060630,3	MCF-7	breast:
2	chr6:38940416..38941559-chr6:39059453..39060636,4	K562	blood:
3	chr6:39054886..39057587-chr6:39057914..39060553,2	MCF-7	breast:
4	chr6:38940785..38941562-chr6:39059873..39060576,3	MCF-7	breast:
5	chr6:39059952..39062322-chr6:39081352..39083480,3	K562	blood:

Variant related genes	Relation type
ENSG00000112167	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs170644	0.86[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs7696	0.96[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv528286	chr6:39019503-39060478	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1031922	chr6:39034484-39060762	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv462919	chr6:39050384-39062990	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv602963	chr6:39050384-39062990	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9968886	C6orf64	cis	multi-tissue	Pritchard
rs9968886	FANCE	cis	parietal	SCAN
rs9968886	C6orf64	cis	Brain Pons	GTEx
rs9968886	C6orf64	cis	Temporal Cortex	GTEx
rs9968886	C6orf64	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39021200-39072000	Weak transcription	Gastric	stomach
2	chr6:39027400-39073000	Weak transcription	Pancreas	Pancrea
3	chr6:39043400-39082000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:39053000-39072400	Weak transcription	Brain Germinal Matrix	brain
5	chr6:39055200-39069800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:39055600-39060800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:39057400-39060800	Weak transcription	Fetal Lung	lung
8	chr6:39058000-39068200	Weak transcription	Thymus	Thymus
9	chr6:39058400-39071200	Weak transcription	Psoas Muscle	Psoas
10	chr6:39058400-39072000	Weak transcription	Left Ventricle	heart
11	chr6:39058400-39072600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:39058400-39073000	Weak transcription	Lung	lung
13	chr6:39059600-39060600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:39059600-39060600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:39059600-39060600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr6:39059800-39061200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:39059800-39062600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:39060000-39061400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:39060400-39061400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:39060400-39073200	Weak transcription	Fetal Heart	heart

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