Variant report

Variant	rs2243115
Chromosome Location	chr3:159706280-159706281
allele	G/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	RAD21	chr3:159706178-159706842	HCT-116	colon:	n/a	chr3:159706491-159706510 chr3:159706496-159706506 chr3:159706496-159706508
2	TCF12	chr3:159706268-159707112	ECC-1	luminal epithelium:	n/a	chr3:159706353-159706361
3	ZBTB7A	chr3:159706277-159706869	ECC-1	luminal epithelium:	n/a	chr3:159706498-159706507
4	YY1	chr3:159706204-159706814	GM12878	blood:	n/a	n/a
5	RELA	chr3:159706273-159706910	GM18951	blood:	n/a	n/a
6	YY1	chr3:159706249-159706601	HCT-116	colon:	n/a	n/a
7	POU2F2	chr3:159706195-159706913	GM12891	blood:	n/a	chr3:159706513-159706525 chr3:159706568-159706580
8	ELF1	chr3:159706250-159706916	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:159706166-159707123	GM18526	blood:	n/a	n/a
10	RAD21	chr3:159706244-159706760	A549	lung:	n/a	chr3:159706491-159706510 chr3:159706496-159706506 chr3:159706496-159706508
11	RUNX3	chr3:159706223-159706951	GM12878	blood:	n/a	n/a
12	CTCF	chr3:159706236-159706713	H1-hESC	embryonic stem cell:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
13	MTA3	chr3:159705808-159707050	GM12878	blood:	n/a	n/a
14	MAX	chr3:159706234-159707179	A549	lung:	n/a	n/a
15	MAX	chr3:159706272-159707159	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:159706264-159707061	GM12878	blood:	n/a	n/a
17	MAFF	chr3:159706119-159706524	HepG2	liver:	n/a	chr3:159706216-159706230
18	TCF12	chr3:159706209-159707216	ECC-1	luminal epithelium:	n/a	chr3:159706353-159706361
19	POLR2A	chr3:159706219-159706847	GM12878	blood:	n/a	n/a
20	MAX	chr3:159706233-159707170	HepG2	liver:	n/a	n/a
21	MAX	chr3:159706271-159707025	SK-N-SH	brain:	n/a	n/a
22	ZNF143	chr3:159706243-159707208	GM12878	blood:	n/a	chr3:159706499-159706509
23	STAT5A	chr3:159706240-159706742	GM12878	blood:	n/a	n/a
24	CTCF	chr3:159706156-159707029	HCT-116	colon:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
25	MAX	chr3:159706229-159707180	MCF-7	breast:	n/a	n/a
26	TCF3	chr3:159706258-159706807	GM12878	blood:	n/a	n/a
27	SMC3	chr3:159706263-159706603	HepG2	liver:	n/a	chr3:159706492-159706506 chr3:159706496-159706506
28	RAD21	chr3:159706244-159706664	SK-N-SH_RA	brain:	n/a	chr3:159706491-159706510 chr3:159706496-159706506 chr3:159706496-159706508
29	WRNIP1	chr3:159706001-159706606	GM12878	blood:	n/a	n/a
30	BCLAF1	chr3:159706252-159706894	GM12878	blood:	n/a	chr3:159706513-159706526 chr3:159706495-159706508 chr3:159706508-159706521
31	CREB1	chr3:159706198-159707037	GM12878	blood:	n/a	n/a
32	RAD21	chr3:159706266-159706701	H1-hESC	embryonic stem cell:	n/a	chr3:159706491-159706510 chr3:159706496-159706506 chr3:159706496-159706508
33	CTCF	chr3:159706196-159706817	MCF-7	breast:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
34	TEAD4	chr3:159706279-159706584	H1-hESC	embryonic stem cell:	n/a	n/a
35	YY1	chr3:159706252-159706761	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:159706181-159707123	GM15510	blood:	n/a	n/a
37	NRF1	chr3:159706259-159706860	GM12878	blood:	n/a	chr3:159706572-159706581
38	MEF2C	chr3:159706212-159706818	GM12878	blood:	n/a	n/a
39	MXI1	chr3:159706055-159707371	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr3:159706259-159706742	IMR90	lung:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
41	CTCF	chr3:159706267-159706832	K562	blood:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
42	RAD21	chr3:159706269-159706628	ECC-1	luminal epithelium:	n/a	chr3:159706491-159706510 chr3:159706496-159706506 chr3:159706496-159706508
43	CTCF	chr3:159706260-159706956	GM12878	blood:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
44	USF2	chr3:159706270-159706501	HepG2	liver:	n/a	n/a
45	SP1	chr3:159706210-159706728	A549	lung:	n/a	chr3:159706572-159706582 chr3:159706516-159706528 chr3:159706572-159706581 chr3:159706571-159706583 chr3:159706517-159706527 chr3:159706573-159706582 chr3:159706517-159706526 chr3:159706571-159706583 chr3:159706518-159706527 chr3:159706573-159706582 chr3:159706568-159706582 chr3:159706572-159706582 chr3:159706518-159706527 chr3:159706516-159706528
46	YY1	chr3:159706266-159706820	GM12892	blood:	n/a	n/a
47	IRF4	chr3:159706231-159706746	GM12878	blood:	n/a	n/a
48	CTCF	chr3:159706262-159706725	H1-hESC	embryonic stem cell:	n/a	chr3:159706586-159706599 chr3:159706490-159706508 chr3:159706491-159706507 chr3:159706493-159706506
49	FOXM1	chr3:159706178-159706929	GM12878	blood:	n/a	n/a
50	E2F6	chr3:159706216-159707230	A549	lung:	n/a	n/a

Variant related genes	Relation type
IL12A	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13319484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322713	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2243136	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243141	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4608735	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs890914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9813028	1.00[YRI][hapmap]

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	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2243115	MLF1	cis	parietal	SCAN
rs2243115	PPM1L	cis	parietal	SCAN
rs2243115	MFSD1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159704000-159706400	Weak transcription	Aorta	Aorta
2	chr3:159705000-159706400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:159705600-159706400	Enhancers	Spleen	Spleen
4	chr3:159705800-159706400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr3:159705800-159706400	Flanking Active TSS	GM12878-XiMat	blood
6	chr3:159705800-159706600	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr3:159706000-159706400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr3:159706000-159706400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:159706000-159706400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr3:159706000-159706400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr3:159706000-159706400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:159706000-159706400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr3:159706000-159706400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:159706000-159706400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr3:159706000-159706400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:159706000-159706400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:159706000-159706400	Enhancers	Liver	Liver
18	chr3:159706000-159706400	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr3:159706000-159706400	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr3:159706000-159706400	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr3:159706000-159706400	Enhancers	Fetal Heart	heart
22	chr3:159706000-159706400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:159706000-159706400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
24	chr3:159706000-159706400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr3:159706000-159706600	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr3:159706000-159706600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr3:159706000-159706600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr3:159706000-159707000	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr3:159706000-159707200	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr3:159706000-159707200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:159706000-159707400	Active TSS	HepG2	liver
32	chr3:159706000-159707600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:159706000-159707600	Active TSS	Rectal Smooth Muscle	rectum
34	chr3:159706000-159707800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr3:159706200-159706400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:159706200-159706400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:159706200-159706400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:159706200-159706400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:159706200-159706400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
40	chr3:159706200-159706400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:159706200-159706400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:159706200-159706400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:159706200-159706400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:159706200-159706400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:159706200-159706400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr3:159706200-159706400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr3:159706200-159706400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:159706200-159706400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:159706200-159706400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:159706200-159706400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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