Variant report

Variant	rs2129470
Chromosome Location	chr5:1936443-1936444
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr5:1936420-1937101	HCT-116	colon:	n/a	chr5:1936717-1936728 chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729
2	MYC	chr5:1936218-1936919	MCF10A-Er-Src	breast:	n/a	n/a
3	SP1	chr5:1936343-1937085	HCT-116	colon:	n/a	n/a
4	NR2F2	chr5:1936413-1936987	MCF-7	breast:	n/a	n/a
5	POLR2A	chr5:1936183-1937575	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr5:1936224-1937326	MCF10A-Er-Src	breast:	n/a	chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729
7	JUND	chr5:1936354-1937015	HCT-116	colon:	n/a	chr5:1936717-1936728 chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729
8	FOSL1	chr5:1936114-1937073	HCT-116	colon:	n/a	chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729
9	FOS	chr5:1936208-1937334	MCF10A-Er-Src	breast:	n/a	chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729
10	STAT3	chr5:1936246-1936820	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr5:1936291-1937357	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr5:1936029-1937335	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr5:1936198-1937350	MCF10A-Er-Src	breast:	n/a	chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729
14	STAT3	chr5:1936344-1936878	MCF10A-Er-Src	breast:	n/a	n/a
15	SP1	chr5:1936313-1937178	HCT-116	colon:	n/a	n/a
16	FOS	chr5:1935965-1937335	MCF10A-Er-Src	breast:	n/a	chr5:1936719-1936727 chr5:1936987-1936999 chr5:1936720-1936731 chr5:1936717-1936729

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1881475..1885354-chr5:1933918..1938503,4	MCF-7	breast:
2	chr5:1936412..1938258-chr5:1944303..1946784,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFS6-13	chr5:1936215-1936660	l_2848_chr5:1936214-1937754_heart

Variant related genes	Relation type
ENSG00000248994	TF binding region
ENSG00000249116	Chromatin interaction
ENSG00000113430	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11956096	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975767	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs4975768	0.92[EUR][1000 genomes]
rs6878830	0.86[EUR][1000 genomes]
rs72706770	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7700710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7737970	0.80[GIH][hapmap]
rs7737997	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv880886	chr5:1880891-1936443	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv880460	chr5:1886471-1936443	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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
7	nsv881650	chr5:1892995-1944487	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv880653	chr5:1892995-1946697	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1015576	chr5:1894124-1942909	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv880562	chr5:1895829-1936443	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv881174	chr5:1895829-1942834	Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv880381	chr5:1895829-1946697	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	nsv980962	chr5:1932426-1945863	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2129470	MRPL36	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1932000-1943200	Weak transcription	Esophagus	oesophagus
2	chr5:1932000-1950800	Weak transcription	Gastric	stomach
3	chr5:1932200-1937600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:1932200-1937600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:1932200-1942200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:1932200-1945600	Weak transcription	Right Ventricle	heart
7	chr5:1932200-1946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:1932400-1936600	Weak transcription	Adipose Nuclei	Adipose
9	chr5:1933000-1938200	Enhancers	HMEC	breast
10	chr5:1933000-1942200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:1934000-1936600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:1934400-1936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:1934400-1942400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:1935200-1938000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:1935400-1945600	Weak transcription	Left Ventricle	heart
16	chr5:1935600-1942200	Weak transcription	Aorta	Aorta
17	chr5:1935600-1950800	Weak transcription	Pancreas	Pancrea
18	chr5:1935800-1938400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:1936000-1938000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:1936000-1941000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:1936000-1942000	Weak transcription	Brain Anterior Caudate	brain
22	chr5:1936000-1942200	Weak transcription	Ovary	ovary
23	chr5:1936200-1936800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:1936400-1937000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:1936400-1937000	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links