Variant report

Variant	rs4254984
Chromosome Location	chr6:39059679-39059680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38941129..38941714-chr6:39059120..39059717,2	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	chr6:38997151..38998027-chr6:39059643..39060342,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs41273118	0.94[ASN][1000 genomes]
rs7696	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296291	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9296292	0.91[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs9462473	0.96[ASN][1000 genomes]
rs9462475	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9462476	0.86[EUR][1000 genomes];0.95[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4254984	PI16	cis	cerebellum	SCAN
rs4254984	C6orf81	cis	cerebellum	SCAN
rs4254984	CCT8	trans	cerebellum	SCAN

Chromatin state (count:22 , 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	chr6:39052600-39060400	Enhancers	Fetal Heart	heart
5	chr6:39053000-39072400	Weak transcription	Brain Germinal Matrix	brain
6	chr6:39055200-39069800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:39055600-39060800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:39057200-39060000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:39057400-39059800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:39057400-39060800	Weak transcription	Fetal Lung	lung
11	chr6:39057800-39059800	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr6:39058000-39068200	Weak transcription	Thymus	Thymus
13	chr6:39058400-39071200	Weak transcription	Psoas Muscle	Psoas
14	chr6:39058400-39072000	Weak transcription	Left Ventricle	heart
15	chr6:39058400-39072600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:39058400-39073000	Weak transcription	Lung	lung
17	chr6:39059000-39060200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:39059600-39060000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:39059600-39060400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:39059600-39060600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:39059600-39060600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:39059600-39060600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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