Variant report

Variant	rs1546252
Chromosome Location	chr5:1796520-1796521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1796401-1798408	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:1796465-1796916	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:1796413-1797143	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr5:1794105-1798433	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:1795858-1798914	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:1796458-1797226	A549	lung:	n/a	n/a
7	POLR2A	chr5:1794704-1797208	IMR90	lung:	n/a	n/a
8	STAT5A	chr5:1796064-1797624	GM12878	blood:	n/a	chr5:1796903-1796915
9	POLR2A	chr5:1795389-1798353	K562	blood:	n/a	n/a
10	POLR2A	chr5:1796428-1797251	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:1795148-1798343	K562	blood:	n/a	n/a
12	POLR2A	chr5:1796399-1797310	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr5:1795095-1798455	GM12891	blood:	n/a	n/a
14	ZNF263	chr5:1795971-1797086	HEK293-T-REx	kidney:	n/a	n/a
15	POLR2A	chr5:1796410-1797316	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:1796397-1798482	GM12891	blood:	n/a	n/a
17	POLR2A	chr5:1796411-1796834	GM12892	blood:	n/a	n/a
18	POLR2A	chr5:1796440-1797776	HL-60	blood:	n/a	n/a
19	POLR2A	chr5:1794429-1798387	Raji	blood:	n/a	n/a
20	POLR2A	chr5:1795870-1798186	GM19193	blood:	n/a	n/a
21	POLR2A	chr5:1795849-1798500	GM12892	blood:	n/a	n/a
22	POLR2A	chr5:1794420-1798546	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr5:1795310-1797914	HEK293	kidney:	n/a	n/a
24	POLR2A	chr5:1795250-1798842	HepG2	liver:	n/a	n/a
25	POLR2A	chr5:1796025-1798395	NB4	blood:	n/a	n/a
26	POLR2A	chr5:1796507-1796878	A549	lung:	n/a	n/a
27	POLR2A	chr5:1796311-1798415	GM12892	blood:	n/a	n/a
28	POLR2A	chr5:1795906-1798390	GM12891	blood:	n/a	n/a
29	POLR2A	chr5:1796504-1796947	A549	lung:	n/a	n/a
30	POLR2A	chr5:1796385-1798404	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr5:1795385-1798427	K562	blood:	n/a	n/a
32	POLR2A	chr5:1795667-1798330	K562	blood:	n/a	n/a
33	POLR2A	chr5:1796445-1798029	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:1796351-1798264	K562	blood:	n/a	n/a
35	POLR2A	chr5:1796391-1798435	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:1796424-1797211	A549	lung:	n/a	n/a
37	POLR2A	chr5:1796442-1796522	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr5:1794860-1798520	K562	blood:	n/a	n/a
39	POLR2A	chr5:1795581-1798300	K562	blood:	n/a	n/a
40	POLR2A	chr5:1795050-1798377	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:1795289-1798422	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr5:1796472-1797652	HepG2	liver:	n/a	n/a
43	POLR2A	chr5:1795342-1801944	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr5:1796042-1797928	GM18505	blood:	n/a	n/a
45	POLR2A	chr5:1795433-1798095	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr5:1795780-1797534	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr5:1795672-1797512	GM19099	blood:	n/a	n/a
48	POLR2A	chr5:1795560-1798480	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr5:1795523-1798583	GM12892	blood:	n/a	n/a
50	POLR2A	chr5:1795584-1798472	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
2	chr5:1762386..1764429-chr5:1795462..1797247,2	K562	blood:
3	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
4	chr5:1769932..1772068-chr5:1795879..1799269,3	MCF-7	breast:
5	chr5:1787615..1789328-chr5:1793761..1797388,3	K562	blood:

No data

Variant related genes	Relation type
NDUFS6	TF binding region
ENSG00000113430	Chromatin interaction
ENSG00000249116	Chromatin interaction
ENSG00000249326	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10074291	0.88[ASN][1000 genomes]
rs10475109	0.88[ASN][1000 genomes]
rs10866526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739312	0.86[ASN][1000 genomes]
rs11740602	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11740753	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11741881	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs11748427	0.89[ASN][1000 genomes]
rs11750565	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12513579	0.95[CEU][hapmap]
rs12513620	0.95[CEU][hapmap]
rs1546253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535295	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17535721	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2131588	0.90[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs2131589	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs2172530	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs2353585	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs3752844	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3756344	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3776152	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3776154	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4147775	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4275010	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296838	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416633	0.89[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs4588629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542979	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62336037	0.80[ASN][1000 genomes]
rs62338060	0.88[ASN][1000 genomes]
rs62338061	0.89[ASN][1000 genomes]
rs62338062	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6859338	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6862914	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864281	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6868515	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6873986	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs6880885	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881253	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]
rs6890404	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894566	0.95[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs7701970	0.88[ASN][1000 genomes]
rs7703762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714300	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	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
7	nsv1020703	chr5:1724199-1814288	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv537608	chr5:1724199-1814288	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	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
10	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1546252	MRPL36	cis	Muscle Skeletal	GTEx
rs1546252	MRPL36	cis	multi-tissue	Pritchard
rs1546252	MRPL36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1790400-1796800	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:1790600-1796600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:1790600-1797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:1790600-1797000	Weak transcription	Fetal Lung	lung
5	chr5:1790600-1797800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:1790800-1796600	Weak transcription	Adipose Nuclei	Adipose
7	chr5:1790800-1797000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:1791000-1796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:1791000-1796600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:1791000-1798800	Weak transcription	Fetal Brain Male	brain
11	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:1791400-1796600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:1791600-1796600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:1792400-1797600	Weak transcription	Fetal Kidney	kidney
15	chr5:1792800-1796800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:1793000-1796800	Weak transcription	K562	blood
17	chr5:1793200-1798800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:1793400-1797000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:1793600-1796600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:1793600-1796600	Weak transcription	Left Ventricle	heart
21	chr5:1793800-1797600	Weak transcription	HUVEC	blood vessel
22	chr5:1794000-1798600	Weak transcription	Stomach Mucosa	stomach
23	chr5:1794400-1796600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:1794400-1797600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:1794400-1798200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:1794400-1799200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:1794600-1796800	Weak transcription	Fetal Heart	heart
28	chr5:1794600-1797000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:1794600-1797000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:1794600-1797200	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:1794600-1797800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:1794600-1798200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:1794600-1799200	Weak transcription	Small Intestine	intestine
34	chr5:1794800-1797400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:1794800-1797400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:1794800-1798800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:1795000-1796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:1795000-1796600	Weak transcription	Colonic Mucosa	Colon
39	chr5:1795000-1797400	Strong transcription	Spleen	Spleen
40	chr5:1795200-1796800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:1795200-1796800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:1795200-1797000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:1795200-1797000	Strong transcription	Fetal Brain Female	brain
44	chr5:1795200-1797000	Weak transcription	Psoas Muscle	Psoas
45	chr5:1795200-1797400	Weak transcription	HepG2	liver
46	chr5:1795200-1797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr5:1795400-1796600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:1795400-1796800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:1795400-1796800	Strong transcription	Brain Germinal Matrix	brain
50	chr5:1795400-1796800	Strong transcription	Fetal Muscle Trunk	muscle

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