Variant report

Variant	rs6555013
Chromosome Location	chr5:1833627-1833628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1830984..1834061-chr5:1881188..1884936,4	MCF-7	breast:
2	chr5:1815435..1817756-chr5:1831860..1834084,2	MCF-7	breast:
3	chr5:1831073..1835336-chr5:1866302..1869597,4	MCF-7	breast:
4	chr5:1797383..1801692-chr5:1833304..1835855,5	MCF-7	breast:
5	chr5:1803153..1805432-chr5:1831999..1834113,2	MCF-7	breast:
6	chr5:1831601..1834486-chr5:1837031..1839898,2	K562	blood:
7	chr5:1830147..1834486-chr5:1837031..1839898,4	K562	blood:
8	chr5:1832864..1834515-chr5:1836517..1838024,2	MCF-7	breast:
9	chr5:1831220..1833843-chr5:1846162..1848165,2	MCF-7	breast:
10	chr5:1830290..1836159-chr5:1836315..1840959,6	MCF-7	breast:
11	chr5:1830811..1833725-chr5:1879674..1882912,3	MCF-7	breast:
12	chr5:1831927..1834401-chr5:1847567..1850200,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000145494	Chromatin interaction
ENSG00000171421	Chromatin interaction
ENSG00000113430	Chromatin interaction
ENSG00000249116	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10037336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045048	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051882	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061246	1.00[CHB][hapmap]
rs10062133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070488	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085096	1.00[CHB][hapmap]
rs10085130	1.00[CHB][hapmap]
rs10474728	1.00[CEU][hapmap]
rs10475110	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475112	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475114	1.00[CEU][hapmap]
rs11505118	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361288	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884830	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402979	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573163	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609097	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883061	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41347149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs464685	0.96[EUR][1000 genomes]
rs58926651	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59515251	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60876329	0.92[EUR][1000 genomes]
rs6861074	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861795	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862330	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866992	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880349	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881273	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881623	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6885220	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888753	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891921	1.00[CHB][hapmap]
rs6895439	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6899016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732314	0.88[EUR][1000 genomes]
rs73734916	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734940	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734941	1.00[ASN][1000 genomes]
rs7707424	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709350	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725178	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924462	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	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
6	nsv461911	chr5:1820557-1855301	Strong transcription Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv596890	chr5:1820557-1855301	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6555013	MRPL36	cis	lymphoblastoid	seeQTL
rs6555013	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1827000-1836800	Weak transcription	Gastric	stomach
2	chr5:1827600-1854000	Weak transcription	Right Atrium	heart
3	chr5:1828400-1834400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:1828600-1836800	Weak transcription	Spleen	Spleen
5	chr5:1828800-1834000	Weak transcription	Dnd41	blood
6	chr5:1828800-1835000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:1829000-1834400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:1831000-1835200	Enhancers	Fetal Heart	heart
9	chr5:1832200-1834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:1832200-1834400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:1832400-1834200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:1832400-1835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:1832600-1834200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:1832800-1834200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:1832800-1834200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:1832800-1836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:1833000-1834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:1833000-1834400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:1833400-1833800	Weak transcription	Right Ventricle	heart
20	chr5:1833600-1834000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr5:1833600-1834000	Weak transcription	Left Ventricle	heart
22	chr5:1833600-1835400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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