Variant report

Variant	rs11953620
Chromosome Location	chr5:1818630-1818631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1812295..1814045-chr5:1818146..1820126,2	MCF-7	breast:
2	chr5:1816258..1819219-chr6:26198199..26201096,2	MCF-7	breast:
3	chr5:1808200..1809817-chr5:1817862..1820260,2	MCF-7	breast:
4	chr5:1814461..1816981-chr5:1818018..1821210,3	MCF-7	breast:
5	chr5:1818595..1823818-chr5:1824144..1826436,4	K562	blood:

Variant related genes	Relation type
ENSG00000197409	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197846	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1018120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10447190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10447191	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11948846	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11959171	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12515616	0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13170104	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13173081	0.85[CHB][hapmap]
rs13178976	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13186705	0.82[CHD][hapmap]
rs2270826	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776147	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776150	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs41411146	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs4975732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975843	0.81[CEU][hapmap]
rs4975846	0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs4975847	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975850	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58460883	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67272124	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6881496	0.82[CHD][hapmap]
rs750495	0.82[CHD][hapmap]

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	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	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11953620	MRPL36	cis	Liver	GTEx
rs11953620	MRPL36	cis	multi-tissue	Pritchard
rs11953620	MRPL36	cis	Muscle Skeletal	GTEx
rs11953620	MRPL36	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1802800-1818800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:1802800-1821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:1802800-1821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:1802800-1822000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr5:1802800-1822800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:1802800-1823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:1802800-1823600	Strong transcription	Primary B cells from cord blood	blood
9	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:1803000-1822400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:1803000-1822400	Strong transcription	A549	lung
15	chr5:1803000-1822600	Strong transcription	Placenta	Placenta
16	chr5:1803000-1822800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:1803000-1822800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:1803000-1822800	Strong transcription	Osteobl	bone
19	chr5:1803000-1823800	Strong transcription	Fetal Thymus	thymus
20	chr5:1803000-1825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr5:1803000-1825000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr5:1803000-1825600	Strong transcription	Liver	Liver
23	chr5:1803000-1826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
26	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
29	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr5:1803200-1819400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:1803200-1821800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:1803200-1822600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:1803200-1823000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:1803200-1825600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:1803200-1825800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
37	chr5:1803400-1821600	Strong transcription	Fetal Stomach	stomach
38	chr5:1803400-1822800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:1803400-1823600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:1803600-1823600	Strong transcription	Hela-S3	cervix
41	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:1803800-1822200	Strong transcription	HepG2	liver
43	chr5:1804000-1825000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:1804200-1822200	Strong transcription	Brain Germinal Matrix	brain
45	chr5:1804200-1823000	Strong transcription	K562	blood
46	chr5:1804200-1824600	Weak transcription	Fetal Brain Male	brain
47	chr5:1804400-1821600	Strong transcription	GM12878-XiMat	blood
48	chr5:1804600-1821600	Strong transcription	Spleen	Spleen
49	chr5:1807200-1819400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr5:1808600-1821800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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