Variant report

Variant	rs4975854
Chromosome Location	chr5:1822326-1822327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1798514..1801939-chr5:1819696..1823981,5	MCF-7	breast:
2	chr5:1820025..1823818-chr5:1823864..1826357,3	K562	blood:
3	chr5:1818595..1823818-chr5:1824144..1826436,4	K562	blood:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 39 )
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];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10447190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10447191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11948846	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11953620	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]
rs11959171	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12515616	0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13170104	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13173081	0.85[CHB][hapmap]
rs13178976	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13186705	0.82[CHD][hapmap]
rs2270826	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776147	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776150	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs41411146	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4975732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975735	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4975843	0.81[CEU][hapmap]
rs4975846	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs4975847	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4975850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58460883	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67272124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6881496	0.82[CHD][hapmap]
rs750495	0.82[CHD][hapmap]

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	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
8	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
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4975854	MRPL36	cis	multi-tissue	Pritchard
rs4975854	MRPL36	cis	Muscle Skeletal	GTEx
rs4975854	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs4975854	MRPL36	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 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	chr5:1802800-1822800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:1802800-1823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:1802800-1823600	Strong transcription	Primary B cells from cord blood	blood
5	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:1803000-1822400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:1803000-1822400	Strong transcription	A549	lung
11	chr5:1803000-1822600	Strong transcription	Placenta	Placenta
12	chr5:1803000-1822800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:1803000-1822800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:1803000-1822800	Strong transcription	Osteobl	bone
15	chr5:1803000-1823800	Strong transcription	Fetal Thymus	thymus
16	chr5:1803000-1825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:1803000-1825000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr5:1803000-1825600	Strong transcription	Liver	Liver
19	chr5:1803000-1826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
22	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
25	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr5:1803200-1822600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:1803200-1823000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:1803200-1825600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr5:1803200-1825800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
31	chr5:1803400-1822800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:1803400-1823600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:1803600-1823600	Strong transcription	Hela-S3	cervix
34	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:1804000-1825000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:1804200-1823000	Strong transcription	K562	blood
37	chr5:1804200-1824600	Weak transcription	Fetal Brain Male	brain
38	chr5:1808600-1825800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:1808800-1825000	Strong transcription	Brain Anterior Caudate	brain
40	chr5:1808800-1826200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:1808800-1826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:1808800-1828800	Strong transcription	Dnd41	blood
43	chr5:1809400-1827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:1809600-1824400	Strong transcription	NHEK	skin
45	chr5:1809800-1826800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:1809800-1828200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:1810000-1826600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:1811200-1825600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:1811400-1823000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr5:1813400-1822400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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