Variant report

Variant	rs4296839
Chromosome Location	chr5:1798413-1798414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1794105-1798433	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:1795858-1798914	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:1795095-1798455	GM12891	blood:	n/a	n/a
4	USF2	chr5:1798307-1798512	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:1796869-1798479	GM12892	blood:	n/a	n/a
6	POLR2A	chr5:1796397-1798482	GM12891	blood:	n/a	n/a
7	POLR2A	chr5:1795849-1798500	GM12892	blood:	n/a	n/a
8	POLR2A	chr5:1794420-1798546	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr5:1795250-1798842	HepG2	liver:	n/a	n/a
10	POLR2A	chr5:1796311-1798415	GM12892	blood:	n/a	n/a
11	POLR2A	chr5:1797599-1798566	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:1798319-1798576	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr5:1795385-1798427	K562	blood:	n/a	n/a
14	POLR2A	chr5:1796391-1798435	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:1794860-1798520	K562	blood:	n/a	n/a
16	HCFC1	chr5:1797935-1802723	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:1795289-1798422	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr5:1795342-1801944	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr5:1795560-1798480	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:1795523-1798583	GM12892	blood:	n/a	n/a
21	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	chr5:1777867..1779395-chr5:1796687..1799686,2	K562	blood:
2	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
3	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
4	chr5:1769932..1772068-chr5:1795879..1799269,3	MCF-7	breast:
5	chr5:1745339..1747054-chr5:1797446..1799846,2	K562	blood:

No data

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

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

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];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133914	1.00[JPT][hapmap]
rs11739312	0.86[ASN][1000 genomes]
rs11740602	0.89[ASN][1000 genomes]
rs11740753	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11741881	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs11748427	0.89[ASN][1000 genomes]
rs11750565	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12513579	0.94[CEU][hapmap]
rs12513620	0.95[CEU][hapmap]
rs1546252	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]
rs1546253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs17535721	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17608534	1.00[JPT][hapmap]
rs2131588	0.89[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs2131589	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs2172530	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs2353585	0.84[CEU][hapmap];0.83[ASN][1000 genomes]
rs3752844	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3756344	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3776152	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3776154	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4147775	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4275010	0.94[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296838	0.98[AFR][1000 genomes];1.00[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];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416633	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs4588629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542979	0.92[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	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6859338	0.88[ASN][1000 genomes]
rs6862914	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864281	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs6868515	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6873986	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs6880885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890404	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894566	0.94[CEU][hapmap];0.91[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];0.93[AMR][1000 genomes];0.99[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
rs4296839	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs4296839	MRPL36	cis	multi-tissue	Pritchard
rs4296839	MRPL36	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1791000-1798800	Weak transcription	Fetal Brain Male	brain
2	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:1793200-1798800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:1794000-1798600	Weak transcription	Stomach Mucosa	stomach
5	chr5:1794400-1799200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:1794600-1799200	Weak transcription	Small Intestine	intestine
7	chr5:1794800-1798800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:1795800-1799000	Strong transcription	Fetal Intestine Small	intestine
9	chr5:1796000-1798600	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr5:1796000-1798600	Strong transcription	Thymus	Thymus
11	chr5:1796000-1798800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:1796000-1798800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:1796000-1798800	Strong transcription	Brain Substantia Nigra	brain
14	chr5:1796000-1799000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
15	chr5:1796200-1798600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:1796200-1798800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:1796200-1798800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:1796200-1798800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:1796400-1798600	Strong transcription	Brain Anterior Caudate	brain
20	chr5:1796400-1798600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:1796400-1798800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:1796400-1798800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:1796400-1798800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:1796400-1798800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:1796400-1798800	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr5:1796400-1798800	Strong transcription	NHEK	skin
27	chr5:1796400-1799000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:1796400-1799000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:1796600-1798600	Strong transcription	Brain Cingulate Gyrus	brain
30	chr5:1796600-1798800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr5:1796600-1798800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:1796600-1798800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr5:1796600-1798800	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr5:1796800-1798600	Strong transcription	NH-A	brain
35	chr5:1796800-1798800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:1796800-1798800	Genic enhancers	Pancreas	Pancrea
37	chr5:1796800-1798800	Strong transcription	HSMMtube	muscle
38	chr5:1796800-1798800	Strong transcription	Osteobl	bone
39	chr5:1796800-1799000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:1796800-1799000	Strong transcription	Fetal Intestine Large	intestine
41	chr5:1796800-1799000	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr5:1796800-1799000	Genic enhancers	Lung	lung
43	chr5:1796800-1799200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:1797000-1798600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:1797000-1798600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:1797000-1798600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:1797000-1798600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:1797000-1798600	Strong transcription	Fetal Lung	lung
49	chr5:1797000-1798600	Genic enhancers	Left Ventricle	heart
50	chr5:1797000-1798800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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