Variant report

Variant	rs17535295
Chromosome Location	chr5:1797350-1797351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 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	USF2	chr5:1797058-1797401	Hela-S3	cervix:	n/a	n/a
3	NFATC1	chr5:1796842-1797396	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:1797193-1797739	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr5:1794105-1798433	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:1795858-1798914	GM12878	blood:	n/a	n/a
7	STAT5A	chr5:1796064-1797624	GM12878	blood:	n/a	chr5:1796903-1796915
8	NFATC1	chr5:1796675-1797353	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:1795389-1798353	K562	blood:	n/a	n/a
10	POLR2A	chr5:1795148-1798343	K562	blood:	n/a	n/a
11	POLR2A	chr5:1796681-1797972	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:1795095-1798455	GM12891	blood:	n/a	n/a
13	POLR2A	chr5:1796869-1798479	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:1796397-1798482	GM12891	blood:	n/a	n/a
15	POLR2A	chr5:1796440-1797776	HL-60	blood:	n/a	n/a
16	POLR2A	chr5:1794429-1798387	Raji	blood:	n/a	n/a
17	POLR2A	chr5:1795870-1798186	GM19193	blood:	n/a	n/a
18	POLR2A	chr5:1795849-1798500	GM12892	blood:	n/a	n/a
19	POLR2A	chr5:1794420-1798546	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr5:1795310-1797914	HEK293	kidney:	n/a	n/a
21	POLR2A	chr5:1795250-1798842	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:1796025-1798395	NB4	blood:	n/a	n/a
23	POLR2A	chr5:1796719-1797374	U87	brain:	n/a	n/a
24	POLR2A	chr5:1796311-1798415	GM12892	blood:	n/a	n/a
25	POLR2A	chr5:1795906-1798390	GM12891	blood:	n/a	n/a
26	POLR2A	chr5:1796385-1798404	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:1795385-1798427	K562	blood:	n/a	n/a
28	POLR2A	chr5:1795667-1798330	K562	blood:	n/a	n/a
29	POLR2A	chr5:1796445-1798029	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:1796351-1798264	K562	blood:	n/a	n/a
31	POLR2A	chr5:1796391-1798435	GM12878	blood:	n/a	n/a
32	POLR2A	chr5:1796577-1798322	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:1794860-1798520	K562	blood:	n/a	n/a
34	POLR2A	chr5:1795581-1798300	K562	blood:	n/a	n/a
35	POLR2A	chr5:1795050-1798377	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:1795289-1798422	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr5:1796472-1797652	HepG2	liver:	n/a	n/a
38	POLR2A	chr5:1795342-1801944	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr5:1796042-1797928	GM18505	blood:	n/a	n/a
40	POLR2A	chr5:1795433-1798095	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr5:1795780-1797534	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr5:1795672-1797512	GM19099	blood:	n/a	n/a
43	POLR2A	chr5:1795560-1798480	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr5:1795523-1798583	GM12892	blood:	n/a	n/a
45	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	chr5:1787615..1789328-chr5:1793761..1797388,3	K562	blood:

No data

Variant related genes	Relation type
NDUFS6	TF binding region
ENSG00000113430	Chromatin interaction
ENSG00000249326	Chromatin interaction
ENSG00000249116	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	0.84[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	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546253	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296838	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296839	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304110	0.99[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	0.83[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	0.93[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	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6873986	0.83[ASN][1000 genomes]
rs6880885	0.81[AFR][1000 genomes];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]
rs6890404	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs17535295	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs17535295	MRPL36	cis	Muscle Skeletal	GTEx
rs17535295	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1790600-1797800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:1791000-1798800	Weak transcription	Fetal Brain Male	brain
3	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:1792400-1797600	Weak transcription	Fetal Kidney	kidney
5	chr5:1793200-1798800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:1793800-1797600	Weak transcription	HUVEC	blood vessel
7	chr5:1794000-1798600	Weak transcription	Stomach Mucosa	stomach
8	chr5:1794400-1797600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:1794400-1798200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:1794400-1799200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:1794600-1797800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:1794600-1798200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:1794600-1799200	Weak transcription	Small Intestine	intestine
14	chr5:1794800-1797400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:1794800-1797400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:1794800-1798800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:1795000-1797400	Strong transcription	Spleen	Spleen
18	chr5:1795200-1797400	Weak transcription	HepG2	liver
19	chr5:1795200-1797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:1795400-1797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:1795400-1798000	Strong transcription	Fetal Stomach	stomach
22	chr5:1795600-1797400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:1795600-1797400	Weak transcription	NHDF-Ad	bronchial
24	chr5:1795800-1797400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:1795800-1799000	Strong transcription	Fetal Intestine Small	intestine
26	chr5:1796000-1797600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:1796000-1797600	Strong transcription	Fetal Thymus	thymus
28	chr5:1796000-1797800	Strong transcription	Primary T cells from cord blood	blood
29	chr5:1796000-1797800	Strong transcription	Gastric	stomach
30	chr5:1796000-1797800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:1796000-1797800	Strong transcription	NHLF	lung
32	chr5:1796000-1798200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:1796000-1798400	Strong transcription	Primary B cells from cord blood	blood
34	chr5:1796000-1798400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:1796000-1798600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr5:1796000-1798600	Strong transcription	Thymus	Thymus
37	chr5:1796000-1798800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:1796000-1798800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:1796000-1798800	Strong transcription	Brain Substantia Nigra	brain
40	chr5:1796000-1799000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr5:1796200-1797400	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr5:1796200-1797600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:1796200-1797600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:1796200-1797800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:1796200-1797800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:1796200-1797800	Strong transcription	Liver	Liver
47	chr5:1796200-1797800	Genic enhancers	GM12878-XiMat	blood
48	chr5:1796200-1797800	Strong transcription	HMEC	breast
49	chr5:1796200-1798200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:1796200-1798200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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