Variant report

Variant	rs154568
Chromosome Location	chr5:89854448-89854449
allele	C/G
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	SIN3AK20	chr5:89854114-89855059	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr5:89854256-89854968	SK-N-SH_RA	brain:	n/a	chr5:89854828-89854837 chr5:89854452-89854466 chr5:89854878-89854892 chr5:89854461-89854475 chr5:89854828-89854842 chr5:89854685-89854699 chr5:89854881-89854895 chr5:89854883-89854892 chr5:89854875-89854889
3	EGR1	chr5:89854420-89855046	ECC-1	luminal epithelium:	n/a	chr5:89854836-89854846 chr5:89854474-89854487 chr5:89854474-89854487 chr5:89854475-89854484 chr5:89854820-89854833
4	POLR2A	chr5:89854083-89854930	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr5:89854036-89855033	MCF-7	breast:	n/a	n/a
6	SIX5	chr5:89854138-89854616	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr5:89853658-89855144	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr5:89853941-89855060	MCF-7	breast:	n/a	n/a
9	NRF1	chr5:89854181-89854628	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr5:89854218-89855016	SK-N-SH_RA	brain:	n/a	chr5:89854828-89854837 chr5:89854452-89854466 chr5:89854878-89854892 chr5:89854461-89854475 chr5:89854828-89854842 chr5:89854685-89854699 chr5:89854881-89854895 chr5:89854883-89854892 chr5:89854875-89854889
11	MYC	chr5:89854265-89854783	MCF-7	breast:	n/a	n/a
12	POLR2A	chr5:89851855-89854488	K562	blood:	n/a	n/a
13	TCF7L2	chr5:89854204-89854959	HCT-116	colon:	n/a	n/a
14	POLR2A	chr5:89854075-89855067	HCT-116	colon:	n/a	n/a
15	USF1	chr5:89854219-89854606	SK-N-SH_RA	brain:	n/a	chr5:89854432-89854448
16	CREB1	chr5:89854248-89854539	A549	lung:	n/a	n/a
17	MAZ	chr5:89854406-89854606	HepG2	liver:	n/a	n/a
18	ELF1	chr5:89854257-89854621	K562	blood:	n/a	chr5:89854459-89854471
19	MAX	chr5:89854133-89855037	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:89854033-89854957	ProgFib	skin:	n/a	n/a
21	TAF1	chr5:89854134-89854884	MCF-7	breast:	n/a	n/a
22	POLR2A	chr5:89854100-89854848	K562	blood:	n/a	n/a
23	TAF1	chr5:89854055-89855115	ECC-1	luminal epithelium:	n/a	n/a
24	CTCF	chr5:89854425-89854461	Kidney_OC	kidney:	n/a	n/a
25	POLR2A	chr5:89854113-89854989	H1-neurons	neurons:	n/a	n/a
26	JUND	chr5:89853918-89855137	SK-N-SH	brain:	n/a	n/a
27	TCF12	chr5:89854048-89855032	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr5:89854161-89855002	H1-neurons	neurons:	n/a	n/a
29	ZMIZ1	chr5:89854320-89854520	K562	blood:	n/a	n/a
30	SP1	chr5:89854103-89854731	A549	lung:	n/a	n/a
31	HMGN3	chr5:89854183-89855047	K562	blood:	n/a	n/a
32	EP300	chr5:89854146-89854714	H1-hESC	embryonic stem cell:	n/a	chr5:89854439-89854455
33	RFX5	chr5:89854236-89854695	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr5:89854134-89854844	K562	blood:	n/a	n/a
35	MAFK	chr5:89854293-89854730	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr5:89854136-89855128	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr5:89854088-89854806	U87	brain:	n/a	n/a
38	YY1	chr5:89854442-89854897	K562	blood:	n/a	chr5:89854828-89854837 chr5:89854452-89854466 chr5:89854878-89854892 chr5:89854461-89854475 chr5:89854828-89854842 chr5:89854685-89854699 chr5:89854881-89854895 chr5:89854883-89854892 chr5:89854875-89854889
39	POLR2A	chr5:89854114-89854911	K562	blood:	n/a	n/a
40	POLR2A	chr5:89854087-89854762	SK-N-MC	brain:	n/a	n/a
41	HCFC1	chr5:89854278-89854762	K562	blood:	n/a	n/a
42	HA-E2F1	chr5:89853294-89855215	MCF-7	breast:	n/a	chr5:89854878-89854888 chr5:89854868-89854883 chr5:89854685-89854694 chr5:89854828-89854837
43	POLR2A	chr5:89854110-89854740	K562	blood:	n/a	n/a
44	IRF1	chr5:89854115-89854688	K562	blood:	n/a	n/a
45	CBX3	chr5:89854155-89854809	K562	blood:	n/a	n/a
46	POLR2A	chr5:89854081-89855039	ECC-1	luminal epithelium:	n/a	n/a
47	SP1	chr5:89853994-89855087	HCT-116	colon:	n/a	chr5:89854858-89854872
48	EGR1	chr5:89854230-89854906	H1-hESC	embryonic stem cell:	n/a	chr5:89854836-89854846 chr5:89854474-89854487 chr5:89854474-89854487 chr5:89854475-89854484 chr5:89854820-89854833
49	BRCA1	chr5:89854184-89855151	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr5:89854147-89855009	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:89854425-89854475	HL-60	blood:	n/a
2	chr5:89854425-89854475	AG04450	lung:	fetal
3	chr5:89854414-89854464	HRE	kidney:	n/a
4	chr5:89854414-89854464	HCPEpiC	choroid plexus:	n/a
5	chr5:89854425-89854475	NH-A	brain:	n/a
6	chr5:89854425-89854475	GM12878	blood:	n/a
7	chr5:89854414-89854464	Caco-2	colon:	n/a
8	chr5:89854414-89854464	CMK	blood:	n/a
9	chr5:89854425-89854475	AG09319	gingival:	n/a
10	chr5:89854425-89854475	HIPEpiC	eye:	n/a
11	chr5:89854414-89854464	U87	brain:	n/a
12	chr5:89854425-89854475	ProgFib	skin:	n/a
13	chr5:89854414-89854464	SK-N-SH	brain:	n/a
14	chr5:89854425-89854475	NT2-D1	testis:	n/a
15	chr5:89854425-89854475	SAEC	small airway:	n/a
16	chr5:89854414-89854464	GM19239	blood:	n/a
17	chr5:89854425-89854475	HCT-116	colon:	n/a
18	chr5:89854414-89854464	K562	blood:	n/a
19	chr5:89854425-89854475	NHBE	bronchial:	n/a
20	chr5:89854414-89854464	NT2-D1	testis:	n/a
21	chr5:89854425-89854475	HCM	heart:	n/a
22	chr5:89854414-89854464	GM12878	blood:	n/a
23	chr5:89854425-89854475	SK-N-SH_RA	brain:	n/a
24	chr5:89854425-89854475	NB4	blood:	n/a
25	chr5:89854425-89854475	Caco-2	colon:	n/a
26	chr5:89854425-89854475	T-47D	breast:	n/a
27	chr5:89854414-89854464	ECC-1	luminal epithelium:	n/a
28	chr5:89854414-89854464	SAEC	small airway:	n/a
29	chr5:89854425-89854475	K562	blood:	n/a
30	chr5:89854414-89854464	BJ	skin:	n/a
31	chr5:89854425-89854475	PrEC	prostate:	n/a
32	chr5:89854414-89854464	T-47D	breast:	n/a
33	chr5:89854425-89854475	HepG2	liver:	n/a
34	chr5:89854414-89854464	H1-hESC	embryonic stem cell:	embryo
35	chr5:89854414-89854464	HEEpiC	esophagus:	n/a
36	chr5:89854425-89854475	RPTEC	kidney:	n/a
37	chr5:89854425-89854475	MCF10A-Er-Src	breast:	n/a
38	chr5:89854414-89854464	AG10803	skin:	n/a
39	chr5:89854425-89854475	Hepatocyte	liver:	n/a
40	chr5:89854425-89854475	Hela-S3	cervix:	n/a
41	chr5:89854425-89854475	HUVEC	blood vessel:	n/a
42	chr5:89854414-89854464	LNCaP	prostate:	n/a
43	chr5:89854414-89854464	GM12892	blood:	n/a
44	chr5:89854414-89854464	PFSK-1	brain:	n/a
45	chr5:89854414-89854464	HAEpiC	amniotic membrane:	n/a
46	chr5:89854425-89854475	BJ	skin:	n/a
47	chr5:89854425-89854475	HMEC	breast:	n/a
48	chr5:89854425-89854475	HAEpiC	amniotic membrane:	n/a
49	chr5:89854414-89854464	PANC-1	pancreas:	n/a
50	chr5:89854414-89854464	HRCEpiC	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
2	chr5:89768685..89771799-chr5:89852676..89855842,6	MCF-7	breast:
3	chr5:89830924..89832784-chr5:89851773..89854511,2	K562	blood:
4	chr5:89703976..89707575-chr5:89854064..89857316,4	K562	blood:
5	chr5:89705231..89707575-chr5:89854422..89857316,5	K562	blood:
6	chr5:89705209..89706757-chr5:89853526..89855162,2	MCF-7	breast:
7	chr5:89769141..89770698-chr5:89851659..89854573,2	K562	blood:
8	chr5:89769550..89772254-chr5:89851679..89856622,6	MCF-7	breast:
9	chr5:89704382..89708328-chr5:89852696..89856618,6	MCF-7	breast:

Variant related genes	Relation type
GPR98	TF binding region
GPR98	CpG island
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000176018	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10069050	0.89[EUR][1000 genomes]
rs154569	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154570	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154572	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154573	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1553545	0.89[EUR][1000 genomes]
rs171790	0.89[EUR][1000 genomes]
rs250377	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs257850	0.89[EUR][1000 genomes]
rs257851	0.90[EUR][1000 genomes]
rs2656957	0.89[EUR][1000 genomes]
rs27201	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs37238	0.89[EUR][1000 genomes]
rs37239	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37240	0.82[EUR][1000 genomes]
rs42467	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs43149	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs491082	0.89[EUR][1000 genomes]
rs511393	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs526806	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs556894	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59159252	0.96[ASN][1000 genomes]
rs594990	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs599432	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs679568	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs810974	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs154568	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89853200-89855200	Active TSS	Fetal Brain Male	brain
2	chr5:89853200-89855600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr5:89853400-89855200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:89853400-89855400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:89853400-89855400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:89853400-89855800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:89853400-89856200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:89853400-89856200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:89853600-89855000	Active TSS	Brain Angular Gyrus	brain
10	chr5:89853600-89855000	Active TSS	Brain Substantia Nigra	brain
11	chr5:89853600-89855000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
12	chr5:89853600-89855200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:89853600-89855200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:89853600-89855200	Active TSS	Pancreas	Pancrea
15	chr5:89853600-89855400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:89853600-89855400	Active TSS	Brain Anterior Caudate	brain
17	chr5:89853600-89856200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr5:89853600-89856600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:89853600-89857600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr5:89853800-89854600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr5:89853800-89855000	Bivalent/Poised TSS	GM12878-XiMat	blood
22	chr5:89853800-89855200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:89853800-89855200	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr5:89853800-89855200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr5:89853800-89855200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:89853800-89855200	Bivalent/Poised TSS	Fetal Kidney	kidney
27	chr5:89853800-89855800	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr5:89853800-89856000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:89853800-89856000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:89853800-89856200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr5:89853800-89858000	Active TSS	K562	blood
32	chr5:89854000-89854600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:89854000-89854600	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr5:89854000-89854600	Bivalent/Poised TSS	NHLF	lung
35	chr5:89854000-89854800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:89854000-89854800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
37	chr5:89854000-89854800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr5:89854000-89854800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
39	chr5:89854000-89855000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:89854000-89855000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:89854000-89855000	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr5:89854000-89855000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:89854000-89855000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:89854000-89855000	Bivalent/Poised TSS	Fetal Lung	lung
45	chr5:89854000-89855000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
46	chr5:89854000-89855000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr5:89854000-89855200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
48	chr5:89854000-89855200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr5:89854000-89855200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
50	chr5:89854000-89855200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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