Variant report

Variant	rs6892790
Chromosome Location	chr5:1948878-1948879
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	chr5:1851660..1854180-chr5:1947393..1949890,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFS6-5	chr5:1948808-1949182	XLOC_004250

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10053882	0.85[CHD][hapmap];0.86[GIH][hapmap]
rs10066840	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6555038	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6555039	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6555040	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv880964	chr5:1912921-1953161	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6892790	TPPP	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1932000-1950800	Weak transcription	Gastric	stomach
2	chr5:1935600-1950800	Weak transcription	Pancreas	Pancrea
3	chr5:1939000-1965600	Weak transcription	Brain Angular Gyrus	brain
4	chr5:1942600-1953800	Weak transcription	Ovary	ovary
5	chr5:1946400-1949000	Weak transcription	Left Ventricle	heart
6	chr5:1946800-1951800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:1947000-1951600	Enhancers	Fetal Heart	heart
8	chr5:1947200-1949000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:1947200-1952200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:1948200-1949000	Enhancers	HMEC	breast
11	chr5:1948400-1949000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:1948400-1949000	Enhancers	Esophagus	oesophagus
13	chr5:1948400-1949000	Enhancers	Fetal Muscle Leg	muscle
14	chr5:1948400-1949200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:1948400-1950000	Enhancers	Right Ventricle	heart
16	chr5:1948400-1950600	Bivalent Enhancer	Fetal Stomach	stomach
17	chr5:1948600-1949000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:1948600-1949400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr5:1948600-1949600	Enhancers	Right Atrium	heart
20	chr5:1948600-1950200	Active TSS	Stomach Smooth Muscle	stomach
21	chr5:1948800-1949000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr5:1948800-1949000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr5:1948800-1949000	Enhancers	NHEK	skin
24	chr5:1948800-1949200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr5:1948800-1949400	Active TSS	Colon Smooth Muscle	Colon

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