Variant report

Variant	rs11574439
Chromosome Location	chr3:46448833-46448834
allele	A/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	HEY1	chr3:46448345-46449103	K562	blood:	n/a	n/a
2	MAX	chr3:46448047-46449447	K562	blood:	n/a	chr3:46448153-46448162
3	ATF1	chr3:46448383-46449169	K562	blood:	n/a	n/a
4	POLR2A	chr3:46448790-46449101	GM12891	blood:	n/a	n/a
5	CEBPB	chr3:46448440-46449065	K562	blood:	n/a	n/a
6	POLR2A	chr3:46448132-46450759	PBDE	blood:	n/a	n/a
7	POLR2A	chr3:46448373-46449180	GM12892	blood:	n/a	n/a
8	EGR1	chr3:46448494-46448886	K562	blood:	n/a	n/a
9	ELF1	chr3:46448335-46449114	K562	blood:	n/a	chr3:46448732-46448743
10	ZNF384	chr3:46448402-46449223	K562	blood:	n/a	n/a
11	YY1	chr3:46448263-46449043	K562	blood:	n/a	chr3:46448296-46448306
12	STAT5A	chr3:46448385-46449068	K562	blood:	n/a	n/a
13	RCOR1	chr3:46447943-46449285	K562	blood:	n/a	n/a
14	CCNT2	chr3:46448078-46449138	K562	blood:	n/a	n/a
15	POLR2A	chr3:46448409-46449336	GM12891	blood:	n/a	n/a
16	POLR2A	chr3:46447845-46449340	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr3:46447985-46449220	K562	blood:	n/a	chr3:46448153-46448162 chr3:46448021-46448031
18	NR2F2	chr3:46447587-46449528	K562	blood:	n/a	n/a
19	ARID3A	chr3:46448396-46449342	K562	blood:	n/a	n/a
20	ETS1	chr3:46448466-46449071	K562	blood:	n/a	n/a
21	POLR2A	chr3:46448504-46449238	U87	brain:	n/a	n/a
22	ELK1	chr3:46448202-46449011	K562	blood:	n/a	n/a
23	PML	chr3:46448300-46449223	K562	blood:	n/a	n/a
24	JUN	chr3:46448021-46449102	HUVEC	blood vessel:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
25	GATA2	chr3:46448487-46448916	K562	blood:	n/a	chr3:46448648-46448655
26	CUX1	chr3:46448117-46449422	K562	blood:	n/a	n/a
27	MAFF	chr3:46448443-46449284	K562	blood:	n/a	n/a
28	ZMIZ1	chr3:46447909-46449216	K562	blood:	n/a	n/a
29	MAX	chr3:46448318-46449152	K562	blood:	n/a	n/a
30	MXI1	chr3:46448389-46449166	K562	blood:	n/a	n/a
31	ZNF143	chr3:46448462-46449320	K562	blood:	n/a	n/a
32	HMGN3	chr3:46448175-46449090	K562	blood:	n/a	n/a
33	EGR1	chr3:46448418-46448843	K562	blood:	n/a	n/a
34	GATA2	chr3:46448432-46449116	K562	blood:	n/a	chr3:46448648-46448655
35	MYC	chr3:46448344-46449216	K562	blood:	n/a	n/a
36	GTF2B	chr3:46448362-46449024	K562	blood:	n/a	n/a
37	MYC	chr3:46448362-46449191	K562	blood:	n/a	n/a
38	UBTF	chr3:46448454-46449148	K562	blood:	n/a	n/a
39	GATA2	chr3:46448439-46448992	K562	blood:	n/a	chr3:46448648-46448655
40	MTA3	chr3:46448217-46449195	GM12878	blood:	n/a	n/a
41	MAFK	chr3:46448378-46449341	K562	blood:	n/a	n/a
42	JUND	chr3:46447939-46449611	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
43	POLR2A	chr3:46448013-46449277	K562	blood:	n/a	n/a
44	CREB1	chr3:46448205-46449227	K562	blood:	n/a	n/a
45	CREB1	chr3:46448069-46449174	K562	blood:	n/a	n/a
46	STAT5A	chr3:46448318-46449090	K562	blood:	n/a	n/a
47	GABPA	chr3:46448309-46448899	HL-60	blood:	n/a	n/a
48	IRF1	chr3:46448264-46449143	K562	blood:	n/a	chr3:46449050-46449071
49	TBP	chr3:46448405-46449188	K562	blood:	n/a	n/a
50	HCFC1	chr3:46447908-46449155	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46447015..46450131-chr3:46450692..46453311,4	K562	blood:
2	chr3:46036059..46037983-chr3:46447594..46449867,2	K562	blood:

Variant related genes	Relation type
CCRL2	TF binding region
ENSG00000223552	TF binding region
ENSG00000121797	Chromatin interaction
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11574431	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11574437	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11574440	1.00[AMR][1000 genomes]
rs11574441	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17141003	1.00[AMR][1000 genomes]
rs17842821	1.00[AMR][1000 genomes]
rs35212534	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3918370	1.00[AMR][1000 genomes]
rs6441969	1.00[AMR][1000 genomes]
rs6776013	0.96[AFR][1000 genomes]
rs6801203	0.96[AFR][1000 genomes]
rs723577	1.00[AMR][1000 genomes]
rs7638702	1.00[AMR][1000 genomes]
rs7640084	1.00[AMR][1000 genomes]
rs7650273	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46438800-46459800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46445000-46450000	Enhancers	Spleen	Spleen
3	chr3:46446200-46450200	Enhancers	Fetal Lung	lung
4	chr3:46446800-46449000	Enhancers	Pancreas	Pancrea
5	chr3:46446800-46450600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:46447200-46449800	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:46447800-46449800	Active TSS	Rectal Smooth Muscle	rectum
8	chr3:46448000-46449600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:46448000-46449800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:46448000-46450000	Enhancers	Brain Substantia Nigra	brain
11	chr3:46448000-46450000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:46448200-46449400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:46448200-46449600	Flanking Active TSS	Fetal Intestine Large	intestine
14	chr3:46448200-46449600	Flanking Active TSS	K562	blood
15	chr3:46448200-46449800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:46448200-46449800	Flanking Active TSS	Hela-S3	cervix
17	chr3:46448200-46450200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:46448200-46452000	Enhancers	Dnd41	blood
19	chr3:46448400-46449000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:46448400-46449200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr3:46448400-46449200	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:46448400-46449400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr3:46448400-46449600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr3:46448400-46449800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr3:46448400-46449800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:46448400-46450000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:46448400-46450000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr3:46448400-46450000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr3:46448400-46450200	Flanking Active TSS	HSMM	muscle
30	chr3:46448400-46450200	Flanking Active TSS	Osteobl	bone
31	chr3:46448400-46450400	Enhancers	Fetal Heart	heart
32	chr3:46448600-46449000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:46448600-46449000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr3:46448600-46449000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:46448600-46449200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:46448600-46449200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr3:46448600-46449200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr3:46448600-46449200	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr3:46448600-46449200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:46448600-46449200	Flanking Active TSS	Placenta	Placenta
41	chr3:46448600-46449200	Active TSS	Thymus	Thymus
42	chr3:46448600-46449400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr3:46448600-46449400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:46448600-46449400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr3:46448600-46449400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr3:46448600-46449400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:46448600-46449400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:46448600-46449400	Flanking Active TSS	Fetal Stomach	stomach
49	chr3:46448600-46449400	Active TSS	Left Ventricle	heart
50	chr3:46448600-46449400	Active TSS	Right Ventricle	heart

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