Variant report

Variant	rs4975735
Chromosome Location	chr5:1830405-1830406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1799884..1801831-chr5:1830027..1832433,4	MCF-7	breast:
2	chr5:1811455..1813099-chr5:1828682..1831578,2	K562	blood:
3	chr5:1830147..1834486-chr5:1837031..1839898,4	K562	blood:
4	chr5:1823993..1826824-chr5:1830176..1831799,2	K562	blood:
5	chr5:1830290..1836159-chr5:1836315..1840959,6	MCF-7	breast:
6	chr5:1823993..1826108-chr5:1830299..1832827,2	K562	blood:

Variant related genes	Relation type
ENSG00000145494	Chromatin interaction
ENSG00000171421	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1018120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10447190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10447191	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11948846	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11953620	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]
rs11959171	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12515616	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13170104	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13173081	0.85[CHB][hapmap]
rs13178976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270826	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3776147	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3776148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3776150	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs41411146	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4975732	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975843	0.81[CEU][hapmap]
rs4975846	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4975847	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975850	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975854	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]
rs58460883	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67272124	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4975735	MRPL36	cis	multi-tissue	Pritchard
rs4975735	MRPL36	cis	Muscle Skeletal	GTEx
rs4975735	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs4975735	MRPL36	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1821800-1831000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:1821800-1832000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:1822200-1830800	Weak transcription	HSMM	muscle
4	chr5:1822200-1831800	Weak transcription	HSMMtube	muscle
5	chr5:1822400-1831600	Weak transcription	HMEC	breast
6	chr5:1822400-1833200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:1822600-1831600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:1822800-1831200	Weak transcription	Osteobl	bone
9	chr5:1825000-1832400	Weak transcription	Brain Anterior Caudate	brain
10	chr5:1825000-1832800	Weak transcription	Brain Substantia Nigra	brain
11	chr5:1825200-1831600	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:1825200-1832600	Weak transcription	Brain Angular Gyrus	brain
13	chr5:1825600-1831400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:1825600-1832400	Weak transcription	Liver	Liver
15	chr5:1825800-1831600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:1826200-1831600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:1826200-1832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:1826400-1831200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:1826400-1831800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:1826600-1830800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:1826600-1831000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:1826600-1831600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:1826600-1833600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:1826800-1830600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:1826800-1831200	Weak transcription	Primary T cells from cord blood	blood
26	chr5:1826800-1831800	Weak transcription	Fetal Intestine Small	intestine
27	chr5:1827000-1830600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:1827000-1831800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:1827000-1833400	Weak transcription	Left Ventricle	heart
30	chr5:1827000-1836800	Weak transcription	Gastric	stomach
31	chr5:1827200-1830600	Weak transcription	Fetal Brain Female	brain
32	chr5:1827200-1833200	Weak transcription	Brain Germinal Matrix	brain
33	chr5:1827600-1831400	Weak transcription	Hela-S3	cervix
34	chr5:1827600-1854000	Weak transcription	Right Atrium	heart
35	chr5:1827800-1830800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:1827800-1830800	Weak transcription	NHLF	lung
37	chr5:1827800-1832600	Weak transcription	Esophagus	oesophagus
38	chr5:1827800-1833400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:1828000-1831400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:1828000-1831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:1828200-1830800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:1828200-1831000	Weak transcription	Right Ventricle	heart
43	chr5:1828200-1831800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:1828400-1831800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:1828400-1834400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:1828600-1830600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:1828600-1830800	Weak transcription	Fetal Stomach	stomach
48	chr5:1828600-1831200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:1828600-1831400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:1828600-1836800	Weak transcription	Spleen	Spleen

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