Variant report

Variant	rs11741881
Chromosome Location	chr5:1832240-1832241
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr5:1801625..1804390-chr5:1831978..1833592,2	K562	blood:
5	chr5:1799884..1801831-chr5:1830027..1832433,4	MCF-7	breast:
6	chr5:1803153..1805432-chr5:1831999..1834113,2	MCF-7	breast:
7	chr5:1827997..1830349-chr5:1831198..1833616,2	K562	blood:
8	chr5:1831601..1834486-chr5:1837031..1839898,2	K562	blood:
9	chr5:1830147..1834486-chr5:1837031..1839898,4	K562	blood:
10	chr5:1831220..1833843-chr5:1846162..1848165,2	MCF-7	breast:
11	chr5:1830290..1836159-chr5:1836315..1840959,6	MCF-7	breast:
12	chr5:1830811..1833725-chr5:1879674..1882912,3	MCF-7	breast:
13	chr5:1823993..1826108-chr5:1830299..1832827,2	K562	blood:
14	chr5:1810746..1813176-chr5:1830895..1832841,2	MCF-7	breast:
15	chr5:1831927..1834401-chr5:1847567..1850200,2	MCF-7	breast:

No data

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

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10074291	0.93[ASN][1000 genomes]
rs10475109	0.93[ASN][1000 genomes]
rs10512646	0.81[CHD][hapmap];0.80[MEX][hapmap]
rs10866526	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs11739312	0.91[ASN][1000 genomes]
rs11740602	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740753	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11748427	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11750565	0.88[EUR][1000 genomes]
rs12513579	0.82[CEU][hapmap];0.81[CHD][hapmap]
rs12513620	0.82[CEU][hapmap]
rs1546252	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs1546253	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs17535295	0.83[ASN][1000 genomes]
rs17535337	0.86[CEU][hapmap];0.93[CHB][hapmap]
rs17535721	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs2131588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172530	0.91[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353585	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752844	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3756344	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776152	0.95[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776154	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4147775	0.88[EUR][1000 genomes]
rs4275010	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs4277951	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs4296838	0.83[ASN][1000 genomes]
rs4296839	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs4304110	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs4416633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588629	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs60542979	0.86[EUR][1000 genomes]
rs62338060	0.93[ASN][1000 genomes]
rs62338061	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62338062	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859338	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6862914	0.83[ASN][1000 genomes]
rs6864281	0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6868515	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6873986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880885	0.83[ASN][1000 genomes]
rs6881253	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs6890404	0.83[ASN][1000 genomes]
rs6894566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701970	0.93[ASN][1000 genomes]
rs7703762	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs7714300	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11741881	MRPL36	cis	Muscle Skeletal	GTEx
rs11741881	MRPL36	cis	lymphoblastoid	seeQTL
rs11741881	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs11741881	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1822400-1833200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:1825000-1832400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:1825000-1832800	Weak transcription	Brain Substantia Nigra	brain
4	chr5:1825200-1832600	Weak transcription	Brain Angular Gyrus	brain
5	chr5:1825600-1832400	Weak transcription	Liver	Liver
6	chr5:1826600-1833600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:1827000-1833400	Weak transcription	Left Ventricle	heart
8	chr5:1827000-1836800	Weak transcription	Gastric	stomach
9	chr5:1827200-1833200	Weak transcription	Brain Germinal Matrix	brain
10	chr5:1827600-1854000	Weak transcription	Right Atrium	heart
11	chr5:1827800-1832600	Weak transcription	Esophagus	oesophagus
12	chr5:1827800-1833400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:1828400-1834400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:1828600-1836800	Weak transcription	Spleen	Spleen
15	chr5:1828800-1834000	Weak transcription	Dnd41	blood
16	chr5:1828800-1835000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:1829000-1834400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:1830200-1832400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr5:1830400-1832800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:1830800-1832800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:1831000-1832400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr5:1831000-1833000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:1831000-1835200	Enhancers	Fetal Heart	heart
24	chr5:1831200-1832400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr5:1831200-1832600	Enhancers	Placenta	Placenta
26	chr5:1831400-1832600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr5:1831600-1832400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:1831800-1832800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr5:1831800-1832800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr5:1831800-1833400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:1831800-1833600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:1832000-1832600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr5:1832000-1832800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:1832000-1832800	Weak transcription	Right Ventricle	heart
35	chr5:1832000-1833000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:1832200-1832400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:1832200-1832400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:1832200-1833000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:1832200-1834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:1832200-1834400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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