Variant report

Variant	rs6890404
Chromosome Location	chr5:1799172-1799173
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1799035-1800569	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:1799154-1802375	MCF10A-Er-Src	breast:	n/a	n/a
3	YY1	chr5:1799100-1800180	HepG2	liver:	n/a	chr5:1799972-1799991 chr5:1799980-1799988 chr5:1799967-1799989 chr5:1799984-1799993 chr5:1799987-1799996 chr5:1799979-1799989 chr5:1799977-1799989 chr5:1799985-1799996
4	POLR2A	chr5:1799089-1802204	HepG2	liver:	n/a	n/a
5	SMC3	chr5:1799133-1799573	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:1799155-1802340	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:1798976-1802439	Hela-S3	cervix:	n/a	n/a
8	SMARCB1	chr5:1799152-1800762	Hela-S3	cervix:	n/a	n/a
9	WRNIP1	chr5:1799128-1799409	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:1799115-1799346	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr5:1799161-1802292	Hela-S3	cervix:	n/a	chr5:1800777-1800786 chr5:1799999-1800008 chr5:1800586-1800595
12	RCOR1	chr5:1799142-1799484	HepG2	liver:	n/a	n/a
13	MAX	chr5:1799055-1801992	HepG2	liver:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
14	MAX	chr5:1799053-1802002	HepG2	liver:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
15	POLR2A	chr5:1799095-1802307	Hela-S3	cervix:	n/a	n/a
16	MAX	chr5:1799111-1802062	NB4	blood:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
17	HEY1	chr5:1799100-1801013	K562	blood:	n/a	chr5:1800043-1800058 chr5:1799985-1800000 chr5:1799511-1799526
18	POLR2A	chr5:1799084-1800764	U87	brain:	n/a	n/a
19	MAZ	chr5:1798962-1800702	IMR90	lung:	n/a	chr5:1800000-1800009 chr5:1799998-1800011 chr5:1799988-1799998 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800000-1800009
20	ZNF384	chr5:1799060-1799173	K562	blood:	n/a	n/a
21	EBF1	chr5:1799077-1799271	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:1799145-1802285	K562	blood:	n/a	n/a
23	MYC	chr5:1799117-1802271	NB4	blood:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
24	POLR2A	chr5:1799060-1802320	HepG2	liver:	n/a	n/a
25	MXI1	chr5:1798908-1802411	SK-N-SH	brain:	n/a	chr5:1800777-1800786 chr5:1799999-1800008 chr5:1800586-1800595
26	MAX	chr5:1799086-1802321	K562	blood:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
27	POLR2A	chr5:1799066-1802383	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr5:1799112-1799617	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:1799016-1800795	HL-60	blood:	n/a	n/a
30	MBD4	chr5:1799160-1799444	HepG2	liver:	n/a	n/a
31	POLR2A	chr5:1799024-1800308	K562	blood:	n/a	n/a
32	POLR2A	chr5:1799093-1800218	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:1799145-1802318	K562	blood:	n/a	n/a
34	POLR2A	chr5:1798951-1802409	GM12878	blood:	n/a	n/a
35	PML	chr5:1799116-1802000	GM12878	blood:	n/a	n/a
36	ELF1	chr5:1799050-1800202	GM12878	blood:	n/a	chr5:1799592-1799604 chr5:1799521-1799533
37	MTA3	chr5:1799032-1799563	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:1799039-1799505	PFSK-1	brain:	n/a	n/a
39	MYC	chr5:1799162-1802378	K562	blood:	n/a	chr5:1800000-1800009 chr5:1800776-1800789 chr5:1799998-1800011 chr5:1800779-1800788 chr5:1799988-1799998 chr5:1800776-1800789 chr5:1799999-1800010 chr5:1799985-1799995 chr5:1800778-1800787 chr5:1800000-1800009 chr5:1800778-1800787 chr5:1800777-1800788 chr5:1800777-1800788 chr5:1800778-1800787
40	POLR2A	chr5:1799063-1800751	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr5:1799032-1800799	U87	brain:	n/a	n/a
42	HCFC1	chr5:1797935-1802723	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr5:1795342-1801944	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr5:1798962-1801953	GM12892	blood:	n/a	n/a
45	POLR2A	chr5:1799024-1802222	Raji	blood:	n/a	n/a
46	UBTF	chr5:1799170-1799775	K562	blood:	n/a	n/a
47	POLR2A	chr5:1798959-1802302	GM12892	blood:	n/a	n/a
48	POLR2A	chr5:1799067-1802249	GM12891	blood:	n/a	n/a
49	MXI1	chr5:1799043-1802137	IMR90	lung:	n/a	chr5:1800777-1800786 chr5:1799999-1800008 chr5:1800586-1800595
50	POLR2A	chr5:1798996-1802067	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:7387129..7388004-chr5:1798958..1799931,2	Hela-S3	cervix:
2	chr17:56707453..56709236-chr5:1799018..1801500,2	MCF-7	breast:
3	chr5:1777867..1779395-chr5:1796687..1799686,2	K562	blood:
4	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
5	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
6	chr5:1769932..1772068-chr5:1795879..1799269,3	MCF-7	breast:
7	chr5:1798942..1801341-chr5:1879541..1882987,3	K562	blood:
8	chr5:1745339..1747054-chr5:1797446..1799846,2	K562	blood:

Variant related genes	Relation type
NDUFS6	TF binding region
ENSG00000249326	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000249116	Chromatin interaction
ENSG00000113430	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10074291	0.88[ASN][1000 genomes]
rs10475109	0.88[ASN][1000 genomes]
rs10866526	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739312	0.86[ASN][1000 genomes]
rs11740602	0.89[ASN][1000 genomes]
rs11740753	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11741881	0.83[ASN][1000 genomes]
rs11748427	0.89[ASN][1000 genomes]
rs11750565	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1546252	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546253	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535295	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535721	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2131588	0.83[ASN][1000 genomes]
rs2131589	0.83[ASN][1000 genomes]
rs2172530	0.81[ASN][1000 genomes]
rs2353585	0.83[ASN][1000 genomes]
rs3752844	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3756344	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3776152	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	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277951	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296838	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416633	0.83[ASN][1000 genomes]
rs4588629	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864281	0.95[ASN][1000 genomes]
rs6868515	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6873986	0.83[ASN][1000 genomes]
rs6880885	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881253	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894566	0.83[ASN][1000 genomes]
rs7701970	0.88[ASN][1000 genomes]
rs7703762	0.93[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
rs6890404	MRPL36	cis	multi-tissue	Pritchard
rs6890404	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs6890404	MRPL36	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1794400-1799200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:1794600-1799200	Weak transcription	Small Intestine	intestine
4	chr5:1796800-1799200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:1797400-1799200	Genic enhancers	Spleen	Spleen
6	chr5:1797600-1799200	Transcr. at gene 5' and 3'	Hela-S3	cervix
7	chr5:1797800-1799200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:1797800-1799200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
9	chr5:1798200-1799200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:1798400-1799200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:1798400-1799200	Weak transcription	Aorta	Aorta
12	chr5:1798400-1799200	Enhancers	Esophagus	oesophagus
13	chr5:1798400-1802400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:1798600-1799200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:1798600-1799200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr5:1798600-1799200	Enhancers	Ovary	ovary
17	chr5:1798600-1799200	Enhancers	Stomach Mucosa	stomach
18	chr5:1798600-1799400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
19	chr5:1798800-1799200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr5:1798800-1799200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:1798800-1799200	Enhancers	Primary B cells from peripheral blood	blood
22	chr5:1798800-1799200	Enhancers	Gastric	stomach
23	chr5:1798800-1799200	Flanking Active TSS	HepG2	liver
24	chr5:1798800-1799200	Flanking Active TSS	HMEC	breast
25	chr5:1798800-1799200	Flanking Active TSS	HSMM	muscle
26	chr5:1798800-1799200	Transcr. at gene 5' and 3'	K562	blood
27	chr5:1798800-1799200	Transcr. at gene 5' and 3'	NHEK	skin
28	chr5:1798800-1799400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:1798800-1799400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:1798800-1799400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr5:1798800-1799400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:1798800-1799400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
33	chr5:1798800-1799400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr5:1798800-1799400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:1798800-1799400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:1798800-1799400	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr5:1798800-1799400	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr5:1798800-1799400	Flanking Active TSS	Fetal Brain Female	brain
39	chr5:1798800-1799600	Flanking Active TSS	Colonic Mucosa	Colon
40	chr5:1798800-1799600	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr5:1798800-1800600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:1798800-1800600	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr5:1798800-1802200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:1798800-1802400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:1798800-1802800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr5:1799000-1799200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:1799000-1799200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:1799000-1799200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
49	chr5:1799000-1799200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr5:1799000-1799200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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