Variant report

Variant	rs2289504
Chromosome Location	chr3:100120850-100120851
allele	C/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	chr3:100119256-100121103	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:100119214-100121034	PBDE	blood:	n/a	n/a
3	POLR2A	chr3:100119234-100120974	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:100119440-100120873	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:100119609-100121584	SK-N-SH	brain:	n/a	n/a
6	WRNIP1	chr3:100119876-100120980	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:100118920-100121749	MCF10A-Er-Src	breast:	n/a	n/a
8	MAZ	chr3:100119719-100120874	K562	blood:	n/a	chr3:100120332-100120342
9	YY1	chr3:100119717-100120983	SK-N-SH	brain:	n/a	chr3:100120170-100120189
10	MAX	chr3:100119167-100120951	NB4	blood:	n/a	chr3:100120332-100120342
11	POLR2A	chr3:100118927-100121609	MCF10A-Er-Src	breast:	n/a	n/a
12	YY1	chr3:100119381-100120884	HepG2	liver:	n/a	chr3:100120170-100120189
13	MAX	chr3:100119637-100120985	H1-hESC	embryonic stem cell:	n/a	chr3:100120332-100120342
14	POLR2A	chr3:100119253-100121011	HL-60	blood:	n/a	n/a
15	TAF1	chr3:100119680-100120929	H1-neurons	neurons:	n/a	n/a
16	STAT5A	chr3:100119628-100120946	GM12878	blood:	n/a	chr3:100120009-100120021
17	POLR2A	chr3:100118252-100121519	K562	blood:	n/a	n/a
18	POLR2A	chr3:100119217-100120898	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr3:100119351-100120939	GM15510	blood:	n/a	n/a
20	POLR2A	chr3:100119710-100120952	GM12891	blood:	n/a	n/a
21	SP1	chr3:100119596-100120981	A549	lung:	n/a	chr3:100120332-100120342 chr3:100120331-100120343 chr3:100120281-100120292 chr3:100120332-100120341 chr3:100120333-100120342 chr3:100120331-100120343 chr3:100120202-100120213 chr3:100120328-100120342 chr3:100120332-100120342
22	TAF1	chr3:100119675-100120956	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr3:100118953-100121748	IMR90	lung:	n/a	chr3:100120332-100120342
24	POLR2A	chr3:100119645-100120878	HepG2	liver:	n/a	n/a
25	E2F4	chr3:100119877-100120949	MCF10A-Er-Src	breast:	n/a	n/a
26	RELA	chr3:100119249-100120989	GM18951	blood:	n/a	n/a
27	POLR2A	chr3:100119690-100120893	U87	brain:	n/a	n/a
28	RUNX3	chr3:100119732-100120912	GM12878	blood:	n/a	n/a
29	ZNF143	chr3:100119769-100120874	K562	blood:	n/a	n/a
30	MYC	chr3:100120811-100120856	K562	blood:	n/a	n/a
31	POLR2A	chr3:100119334-100120900	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:100119582-100121040	Hela-S3	cervix:	n/a	n/a
33	BCLAF1	chr3:100119690-100120941	GM12878	blood:	n/a	chr3:100120029-100120038
34	RUNX3	chr3:100119698-100120860	GM12878	blood:	n/a	n/a
35	MYBL2	chr3:100119592-100120910	HepG2	liver:	n/a	chr3:100120427-100120442
36	POLR2A	chr3:100119719-100120975	H1-hESC	embryonic stem cell:	n/a	n/a
37	CEBPB	chr3:100119756-100120854	Hela-S3	cervix:	n/a	n/a
38	MYBL2	chr3:100119665-100121071	HepG2	liver:	n/a	chr3:100120427-100120442
39	USF2	chr3:100119834-100120993	Hela-S3	cervix:	n/a	n/a
40	MAX	chr3:100119462-100120854	HCT-116	colon:	n/a	chr3:100120332-100120342
41	E2F6	chr3:100119705-100120886	K562	blood:	n/a	chr3:100120283-100120294
42	POLR2A	chr3:100119651-100121401	HEK293	kidney:	n/a	n/a
43	MAX	chr3:100119644-100120906	H1-hESC	embryonic stem cell:	n/a	chr3:100120332-100120342
44	POLR2A	chr3:100119211-100120944	HL-60	blood:	n/a	n/a
45	MYC	chr3:100119583-100121273	A549	lung:	n/a	chr3:100120332-100120342
46	POLR2A	chr3:100119512-100120988	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr3:100119720-100120859	GM12891	blood:	n/a	n/a
48	HCFC1	chr3:100118890-100122089	Hela-S3	cervix:	n/a	n/a
49	HEY1	chr3:100119732-100120962	K562	blood:	n/a	n/a
50	POLR2A	chr3:100119037-100121014	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100079303..100082344-chr3:100118989..100121864,3	K562	blood:
2	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:
3	chr3:100120411..100122999-chr3:100364924..100367578,2	K562	blood:
4	chr3:100120464..100122813-chr3:100141808..100145050,3	K562	blood:
5	chr3:100120119..100120883-chr4:140098243..140098989,2	NB4	blood:
6	chr3:100118702..100121299-chr3:100427057..100432444,4	K562	blood:
7	chr3:100033941..100036861-chr3:100119084..100121565,2	MCF-7	breast:
8	chr17:57182962..57185099-chr3:100120179..100122851,2	MCF-7	breast:
9	chr3:100119962..100120935-chr8:144635246..144635884,2	Hela-S3	cervix:
10	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
11	chr17:16118623..16119597-chr3:100120034..100120875,2	Hela-S3	cervix:
12	chr3:100118496..100120943-chr3:101229402..101232050,2	K562	blood:
13	chr3:99979418..99981870-chr3:100118340..100121144,2	K562	blood:
14	chr3:100119980..100121652-chr3:101394464..101397120,2	K562	blood:
15	chr1:165667298..165667923-chr3:100120364..100120890,2	NB4	blood:
16	chr3:99985781..99987839-chr3:100119283..100121257,2	K562	blood:
17	chr3:100099401..100103527-chr3:100117550..100121361,6	MCF-7	breast:
18	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:
19	chr3:99535287..99537035-chr3:100119228..100122105,2	MCF-7	breast:
20	chr3:100120818..100123698-chr3:100370041..100372201,2	K562	blood:
21	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:

Variant related genes	Relation type
TOMM70A	TF binding region
ENSG00000143149	Chromatin interaction
ENSG00000114354	Chromatin interaction
ENSG00000256628	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000109381	Chromatin interaction
ENSG00000252989	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000066422	Chromatin interaction
ENSG00000036054	Chromatin interaction
ENSG00000141027	Chromatin interaction
ENSG00000138468	Chromatin interaction
ENSG00000273488	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000184220	Chromatin interaction
ENSG00000104518	Chromatin interaction
ENSG00000224738	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1036769	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711112	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214374	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696105	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289503	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316701	0.83[EUR][1000 genomes]
rs277621	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277627	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs277631	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277640	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277646	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277648	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277649	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378535	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421855	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928171	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781422	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784494	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2289504	LNP1	cis	Thyroid	GTEx
rs2289504	LOC348801	Cis_1M	lymphoblastoid	RTeQTL
rs2289504	LNP1	cis	Esophagus Muscularis	GTEx
rs2289504	LNP1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100116800-100121600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:100117000-100123000	Active TSS	K562	blood
3	chr3:100117600-100121000	Active TSS	Fetal Kidney	kidney
4	chr3:100117800-100122800	Active TSS	Right Atrium	heart
5	chr3:100118200-100122000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:100118200-100122000	Active TSS	Left Ventricle	heart
7	chr3:100118200-100122400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:100118200-100122400	Active TSS	HSMMtube	muscle
9	chr3:100118200-100122600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:100118200-100122600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:100118200-100123400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:100118200-100123600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:100118400-100122600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:100118400-100122600	Active TSS	Fetal Intestine Large	intestine
15	chr3:100118400-100122600	Active TSS	NHDF-Ad	bronchial
16	chr3:100118400-100123000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:100118400-100123000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:100118400-100123000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:100118400-100123000	Active TSS	NHLF	lung
20	chr3:100118600-100121000	Active TSS	Gastric	stomach
21	chr3:100118600-100122000	Bivalent/Poised TSS	HepG2	liver
22	chr3:100118600-100123000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr3:100118800-100121000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:100118800-100121000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:100118800-100121000	Active TSS	Esophagus	oesophagus
26	chr3:100118800-100121600	Active TSS	A549	lung
27	chr3:100118800-100121600	Active TSS	HMEC	breast
28	chr3:100118800-100121800	Active TSS	Fetal Intestine Small	intestine
29	chr3:100118800-100121800	Active TSS	Ovary	ovary
30	chr3:100118800-100122000	Active TSS	Aorta	Aorta
31	chr3:100118800-100122000	Active TSS	Right Ventricle	heart
32	chr3:100118800-100122200	Active TSS	Fetal Lung	lung
33	chr3:100118800-100122200	Active TSS	Fetal Stomach	stomach
34	chr3:100118800-100122400	Active TSS	Colonic Mucosa	Colon
35	chr3:100118800-100122600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:100118800-100122600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:100118800-100122600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:100118800-100123000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:100118800-100123400	Active TSS	GM12878-XiMat	blood
40	chr3:100119000-100121000	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr3:100119000-100121000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:100119000-100121000	Active TSS	Lung	lung
43	chr3:100119000-100121000	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr3:100119000-100121200	Active TSS	Muscle Satellite Cultured Cells	--
45	chr3:100119000-100121200	Active TSS	Placenta Amnion	Placenta Amnion
46	chr3:100119000-100121200	Active TSS	Dnd41	blood
47	chr3:100119000-100121600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:100119000-100121600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:100119000-100121600	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:100119000-100121600	Active TSS	Stomach Mucosa	stomach

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