Variant report

Variant	rs2289503
Chromosome Location	chr3:100121121-100121122
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	chr3:100119609-100121584	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:100118920-100121749	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:100118927-100121609	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:100118252-100121519	K562	blood:	n/a	n/a
5	STAT3	chr3:100121094-100121439	MCF10A-Er-Src	breast:	n/a	n/a
6	MAZ	chr3:100118953-100121748	IMR90	lung:	n/a	chr3:100120332-100120342
7	POLR2A	chr3:100119651-100121401	HEK293	kidney:	n/a	n/a
8	POLR2A	chr3:100121008-100121379	U87	brain:	n/a	n/a
9	MYC	chr3:100119583-100121273	A549	lung:	n/a	chr3:100120332-100120342
10	HCFC1	chr3:100118890-100122089	Hela-S3	cervix:	n/a	n/a
11	GATA2	chr3:100119846-100121503	SH-SY5Y	brain:	n/a	chr3:100120540-100120550 chr3:100120537-100120553 chr3:100120534-100120555 chr3:100120537-100120553 chr3:100120593-100120602
12	TBP	chr3:100119736-100121501	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:100119229-100121393	K562	blood:	n/a	n/a
14	RFX5	chr3:100119739-100121493	Hela-S3	cervix:	n/a	chr3:100121320-100121334 chr3:100121322-100121336
15	POLR2A	chr3:100119112-100121696	SK-N-MC	brain:	n/a	n/a
16	SIN3A	chr3:100118787-100121306	H1-hESC	embryonic stem cell:	n/a	n/a
17	IRF1	chr3:100119757-100121359	K562	blood:	n/a	chr3:100120080-100120094 chr3:100120331-100120345
18	MAX	chr3:100119070-100121123	A549	lung:	n/a	chr3:100120332-100120342
19	POLR2A	chr3:100118986-100121840	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:100121048-100121461	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:100119491-100121465	U87	brain:	n/a	n/a
22	STAT3	chr3:100121120-100121379	MCF10A-Er-Src	breast:	n/a	n/a
23	CHD1	chr3:100119903-100121330	GM12878	blood:	n/a	n/a
24	MAFK	chr3:100119811-100121174	K562	blood:	n/a	chr3:100120701-100120718
25	MAFK	chr3:100119787-100121336	Hela-S3	cervix:	n/a	chr3:100120701-100120718
26	POLR2A	chr3:100119200-100121230	PANC-1	pancreas:	n/a	n/a
27	MXI1	chr3:100118433-100122085	IMR90	lung:	n/a	n/a
28	MXI1	chr3:100118461-100122114	SK-N-SH	brain:	n/a	n/a
29	REST	chr3:100119145-100121269	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr3:100119205-100121407	Raji	blood:	n/a	n/a
31	POLR2A	chr3:100118877-100121951	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:100119662-100121574	K562	blood:	n/a	n/a
33	POLR2A	chr3:100120946-100121654	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr3:100120993-100121397	U87	brain:	n/a	n/a
35	MYC	chr3:100121086-100121479	MCF10A-Er-Src	breast:	n/a	n/a
36	GATA1	chr3:100119885-100121133	PBDE	blood:	n/a	chr3:100120540-100120550 chr3:100120537-100120553 chr3:100120534-100120555 chr3:100120537-100120553 chr3:100120593-100120602
37	BACH1	chr3:100120997-100121464	K562	blood:	n/a	n/a
38	MAZ	chr3:100119727-100121165	GM12878	blood:	n/a	chr3:100120332-100120342
39	POLR2A	chr3:100118213-100122018	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:100119652-100121832	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:100119269-100121451	GM18505	blood:	n/a	n/a
42	EP300	chr3:100119803-100121247	GM12878	blood:	n/a	chr3:100120030-100120037
43	CHD1	chr3:100119941-100122591	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:100121095-100121368	ProgFib	skin:	n/a	n/a
45	BRCA1	chr3:100119864-100121268	Hela-S3	cervix:	n/a	n/a
46	HEY1	chr3:100119569-100121129	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:100119375-100121338	GM18526	blood:	n/a	n/a
48	POLR2A	chr3:100119171-100121469	HepG2	liver:	n/a	n/a
49	MAX	chr3:100119287-100121540	Hela-S3	cervix:	n/a	chr3:100120332-100120342
50	POLR2A	chr3:100119116-100121370	Hela-S3	cervix:	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	chr3:100118702..100121299-chr3:100427057..100432444,4	K562	blood:
6	chr3:100033941..100036861-chr3:100119084..100121565,2	MCF-7	breast:
7	chr17:57182962..57185099-chr3:100120179..100122851,2	MCF-7	breast:
8	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
9	chr3:99979418..99981870-chr3:100118340..100121144,2	K562	blood:
10	chr3:100119980..100121652-chr3:101394464..101397120,2	K562	blood:
11	chr3:99985781..99987839-chr3:100119283..100121257,2	K562	blood:
12	chr3:100099401..100103527-chr3:100117550..100121361,6	MCF-7	breast:
13	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:
14	chr3:99535287..99537035-chr3:100119228..100122105,2	MCF-7	breast:
15	chr3:100120818..100123698-chr3:100370041..100372201,2	K562	blood:
16	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:

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

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1036769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711112	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1214374	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696105	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119686	0.80[AMR][1000 genomes]
rs2289504	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	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277627	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs277631	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277640	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277646	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277648	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277649	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs378535	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421855	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928171	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781422	0.97[AFR][1000 genomes];0.97[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
rs2289503	LNP1	cis	Muscle Skeletal	GTEx
rs2289503	LNP1	cis	Thyroid	GTEx
rs2289503	LNP1	cis	Esophagus Muscularis	GTEx
rs2289503	LOC348801	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr3:100117800-100122800	Active TSS	Right Atrium	heart
4	chr3:100118200-100122000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:100118200-100122000	Active TSS	Left Ventricle	heart
6	chr3:100118200-100122400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:100118200-100122400	Active TSS	HSMMtube	muscle
8	chr3:100118200-100122600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:100118200-100122600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:100118200-100123400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:100118200-100123600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:100118400-100122600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:100118400-100122600	Active TSS	Fetal Intestine Large	intestine
14	chr3:100118400-100122600	Active TSS	NHDF-Ad	bronchial
15	chr3:100118400-100123000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:100118400-100123000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:100118400-100123000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr3:100118400-100123000	Active TSS	NHLF	lung
19	chr3:100118600-100122000	Bivalent/Poised TSS	HepG2	liver
20	chr3:100118600-100123000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:100118800-100121600	Active TSS	A549	lung
22	chr3:100118800-100121600	Active TSS	HMEC	breast
23	chr3:100118800-100121800	Active TSS	Fetal Intestine Small	intestine
24	chr3:100118800-100121800	Active TSS	Ovary	ovary
25	chr3:100118800-100122000	Active TSS	Aorta	Aorta
26	chr3:100118800-100122000	Active TSS	Right Ventricle	heart
27	chr3:100118800-100122200	Active TSS	Fetal Lung	lung
28	chr3:100118800-100122200	Active TSS	Fetal Stomach	stomach
29	chr3:100118800-100122400	Active TSS	Colonic Mucosa	Colon
30	chr3:100118800-100122600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:100118800-100122600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:100118800-100122600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:100118800-100123000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:100118800-100123400	Active TSS	GM12878-XiMat	blood
35	chr3:100119000-100121200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:100119000-100121200	Active TSS	Placenta Amnion	Placenta Amnion
37	chr3:100119000-100121200	Active TSS	Dnd41	blood
38	chr3:100119000-100121600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:100119000-100121600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:100119000-100121600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:100119000-100121600	Active TSS	Stomach Mucosa	stomach
42	chr3:100119000-100121800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:100119000-100121800	Active TSS	Psoas Muscle	Psoas
44	chr3:100119000-100122000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:100119000-100122000	Active TSS	HSMM	muscle
46	chr3:100119000-100122200	Active TSS	Fetal Muscle Trunk	muscle
47	chr3:100119000-100122200	Active TSS	Hela-S3	cervix
48	chr3:100119000-100122600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:100119000-100122600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:100119000-100122800	Active TSS	HUES48 Cell Line	embryonic stem cell

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