Variant report

Variant	rs2289500
Chromosome Location	chr3:100119137-100119138
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:100118920-100121749	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:100118927-100121609	MCF10A-Er-Src	breast:	n/a	n/a
3	SIN3AK20	chr3:100119044-100120679	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr3:100119112-100119522	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:100118252-100121519	K562	blood:	n/a	n/a
6	MAZ	chr3:100118953-100121748	IMR90	lung:	n/a	chr3:100120332-100120342
7	HCFC1	chr3:100118890-100122089	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr3:100119037-100121014	GM12878	blood:	n/a	n/a
9	SIN3AK20	chr3:100119108-100120860	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr3:100119103-100119589	A549	lung:	n/a	n/a
11	CTCF	chr3:100119120-100119270	GM12872	blood:	n/a	n/a
12	POLR2A	chr3:100119112-100121696	SK-N-MC	brain:	n/a	n/a
13	SIN3A	chr3:100118787-100121306	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr3:100119070-100121123	A549	lung:	n/a	chr3:100120332-100120342
15	POLR2A	chr3:100118986-100121840	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:100119085-100121001	GM12892	blood:	n/a	n/a
17	HA-E2F1	chr3:100119123-100120918	MCF-7	breast:	n/a	n/a
18	MXI1	chr3:100118433-100122085	IMR90	lung:	n/a	n/a
19	MXI1	chr3:100118461-100122114	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:100118940-100120898	HUVEC	blood vessel:	n/a	n/a
21	WRNIP1	chr3:100118812-100119579	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:100118877-100121951	GM12891	blood:	n/a	n/a
23	SIN3AK20	chr3:100119120-100119411	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:100118213-100122018	HepG2	liver:	n/a	n/a
25	SIN3AK20	chr3:100118847-100120979	MCF-7	breast:	n/a	n/a
26	POLR2A	chr3:100119093-100120947	GM12892	blood:	n/a	n/a
27	CHD1	chr3:100119119-100119601	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:100119116-100121370	Hela-S3	cervix:	n/a	n/a
29	MAFF	chr3:100119054-100119358	K562	blood:	n/a	n/a
30	POLR2A	chr3:100119129-100121271	GM19099	blood:	n/a	n/a
31	POLR2A	chr3:100119101-100121708	IMR90	lung:	n/a	n/a
32	POLR2A	chr3:100118885-100119597	GM12878	blood:	n/a	n/a
33	MXI1	chr3:100118905-100120707	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

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	chr3:100117960..100119967-chr3:100122961..100124652,2	K562	blood:
4	chr3:100118702..100121299-chr3:100427057..100432444,4	K562	blood:
5	chr3:100033941..100036861-chr3:100119084..100121565,2	MCF-7	breast:
6	chr3:99541055..99543601-chr3:100118284..100119899,2	K562	blood:
7	chr3:100106736..100109063-chr3:100117268..100119845,2	K562	blood:
8	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
9	chr3:100118496..100120943-chr3:101229402..101232050,2	K562	blood:
10	chr3:99979418..99981870-chr3:100118340..100121144,2	K562	blood:
11	chr3:100093392..100095134-chr3:100117257..100119612,2	K562	blood:
12	chr3:99996650..99998446-chr3:100117737..100119944,2	K562	blood:
13	chr3:100099401..100103527-chr3:100117550..100121361,6	MCF-7	breast:
14	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:

No data

Variant related genes	Relation type
LNP1	TF binding region
ENSG00000273488	Chromatin interaction
ENSG00000036054	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000138468	Chromatin interaction
ENSG00000114354	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1214377	0.82[ASN][1000 genomes]
rs1661287	0.86[ASN][1000 genomes]
rs2316264	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277632	0.86[ASN][1000 genomes]
rs277639	0.86[ASN][1000 genomes]
rs277641	0.86[ASN][1000 genomes]
rs277647	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6797836	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941470	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289500	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs2289500	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr3:100117600-100119600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr3:100117600-100121000	Active TSS	Fetal Kidney	kidney
5	chr3:100117800-100119200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:100117800-100119200	Flanking Active TSS	Liver	Liver
7	chr3:100117800-100119400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:100117800-100119400	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr3:100117800-100122800	Active TSS	Right Atrium	heart
10	chr3:100118000-100119400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:100118200-100119200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:100118200-100119200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr3:100118200-100119200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:100118200-100119200	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr3:100118200-100119200	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr3:100118200-100119200	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr3:100118200-100119200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:100118200-100119200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr3:100118200-100119200	Flanking Active TSS	Fetal Brain Male	brain
20	chr3:100118200-100119200	Flanking Active TSS	Fetal Thymus	thymus
21	chr3:100118200-100119200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr3:100118200-100119200	Flanking Active TSS	HUVEC	blood vessel
23	chr3:100118200-100119200	Flanking Active TSS	Osteobl	bone
24	chr3:100118200-100119400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr3:100118200-100119400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr3:100118200-100119400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr3:100118200-100119400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr3:100118200-100119400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr3:100118200-100119600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:100118200-100119800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr3:100118200-100120000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:100118200-100122000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:100118200-100122000	Active TSS	Left Ventricle	heart
34	chr3:100118200-100122400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:100118200-100122400	Active TSS	HSMMtube	muscle
36	chr3:100118200-100122600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:100118200-100122600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:100118200-100123400	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr3:100118200-100123600	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr3:100118400-100119200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:100118400-100119200	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr3:100118400-100119200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:100118400-100119200	Flanking Active TSS	Thymus	Thymus
44	chr3:100118400-100119400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr3:100118400-100119400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:100118400-100119400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr3:100118400-100119400	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr3:100118400-100119400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr3:100118400-100119600	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:100118400-100119600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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