Variant report

Variant	rs11574438
Chromosome Location	chr3:46448435-46448436
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	chr3:46448132-46450759	PBDE	blood:	n/a	n/a
5	POLR2A	chr3:46448373-46449180	GM12892	blood:	n/a	n/a
6	CREB1	chr3:46448295-46448734	GM12878	blood:	n/a	n/a
7	ELF1	chr3:46448335-46449114	K562	blood:	n/a	chr3:46448732-46448743
8	ZNF384	chr3:46448402-46449223	K562	blood:	n/a	n/a
9	YY1	chr3:46448263-46449043	K562	blood:	n/a	chr3:46448296-46448306
10	STAT5A	chr3:46448385-46449068	K562	blood:	n/a	n/a
11	RCOR1	chr3:46447943-46449285	K562	blood:	n/a	n/a
12	CCNT2	chr3:46448078-46449138	K562	blood:	n/a	n/a
13	POLR2A	chr3:46448409-46449336	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:46447845-46449340	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr3:46447985-46449220	K562	blood:	n/a	chr3:46448153-46448162 chr3:46448021-46448031
16	NR2F2	chr3:46447587-46449528	K562	blood:	n/a	n/a
17	ARID3A	chr3:46448396-46449342	K562	blood:	n/a	n/a
18	ELK1	chr3:46448202-46449011	K562	blood:	n/a	n/a
19	PML	chr3:46448300-46449223	K562	blood:	n/a	n/a
20	JUN	chr3:46448021-46449102	HUVEC	blood vessel:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
21	CUX1	chr3:46448117-46449422	K562	blood:	n/a	n/a
22	ZMIZ1	chr3:46447909-46449216	K562	blood:	n/a	n/a
23	MAX	chr3:46448318-46449152	K562	blood:	n/a	n/a
24	MXI1	chr3:46448389-46449166	K562	blood:	n/a	n/a
25	HMGN3	chr3:46448175-46449090	K562	blood:	n/a	n/a
26	SPI1	chr3:46448432-46448777	GM12891	blood:	n/a	n/a
27	EGR1	chr3:46448418-46448843	K562	blood:	n/a	n/a
28	GATA2	chr3:46448432-46449116	K562	blood:	n/a	chr3:46448648-46448655
29	MYC	chr3:46448344-46449216	K562	blood:	n/a	n/a
30	GTF2B	chr3:46448362-46449024	K562	blood:	n/a	n/a
31	MYC	chr3:46448362-46449191	K562	blood:	n/a	n/a
32	MTA3	chr3:46448217-46449195	GM12878	blood:	n/a	n/a
33	MAFK	chr3:46448378-46449341	K562	blood:	n/a	n/a
34	JUND	chr3:46447939-46449611	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
35	POLR2A	chr3:46448013-46449277	K562	blood:	n/a	n/a
36	BACH1	chr3:46448433-46448777	K562	blood:	n/a	n/a
37	CREB1	chr3:46448205-46449227	K562	blood:	n/a	n/a
38	CREB1	chr3:46448069-46449174	K562	blood:	n/a	n/a
39	STAT5A	chr3:46448318-46449090	K562	blood:	n/a	n/a
40	GABPA	chr3:46448309-46448899	HL-60	blood:	n/a	n/a
41	IRF1	chr3:46448264-46449143	K562	blood:	n/a	chr3:46449050-46449071
42	TBP	chr3:46448405-46449188	K562	blood:	n/a	n/a
43	USF1	chr3:46448332-46448779	K562	blood:	n/a	n/a
44	HCFC1	chr3:46447908-46449155	K562	blood:	n/a	n/a
45	CHD2	chr3:46448172-46449017	K562	blood:	n/a	n/a
46	TRIM28	chr3:46448250-46449202	K562	blood:	n/a	n/a
47	HDAC2	chr3:46448359-46448916	K562	blood:	n/a	n/a
48	POLR2A	chr3:46448304-46449115	K562	blood:	n/a	n/a
49	TAF1	chr3:46448358-46449131	K562	blood:	n/a	n/a
50	SPI1	chr3:46448354-46448732	GM12891	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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTF-1	chr3:46448388-46448550	ENSG00000223552.1

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10490771	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11574432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11574444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11575823	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1607738	0.85[AMR][1000 genomes]
rs17078932	0.85[AMR][1000 genomes]
rs17078949	0.85[AMR][1000 genomes]
rs17141109	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17141112	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28584272	0.85[AMR][1000 genomes]
rs34158148	0.82[AFR][1000 genomes]
rs3918378	1.00[AMR][1000 genomes]
rs3918383	1.00[AMR][1000 genomes]
rs3918386	1.00[AMR][1000 genomes]
rs41469351	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41475349	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41499550	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4463007	0.87[AMR][1000 genomes]
rs57571354	0.85[AMR][1000 genomes]
rs58970771	0.85[AMR][1000 genomes]
rs59568150	0.85[AMR][1000 genomes]
rs60700685	0.85[AMR][1000 genomes]
rs61151866	0.85[AMR][1000 genomes]
rs61389423	0.85[AMR][1000 genomes]
rs61550542	0.85[AMR][1000 genomes]
rs61740461	0.85[AMR][1000 genomes]
rs72900271	0.85[AMR][1000 genomes]
rs72900273	0.85[AMR][1000 genomes]
rs72900285	0.85[AMR][1000 genomes]
rs72900298	0.85[AMR][1000 genomes]
rs72902113	0.85[AMR][1000 genomes]
rs72902116	0.85[AMR][1000 genomes]
rs72902152	0.85[AMR][1000 genomes]
rs72904172	0.85[AMR][1000 genomes]
rs72906018	0.85[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:81 , 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	chr3:46445000-46448600	Enhancers	Fetal Intestine Small	intestine
3	chr3:46445000-46450000	Enhancers	Spleen	Spleen
4	chr3:46445800-46448600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:46446000-46448600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:46446200-46448600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:46446200-46448600	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr3:46446200-46448600	Enhancers	Right Atrium	heart
9	chr3:46446200-46450200	Enhancers	Fetal Lung	lung
10	chr3:46446400-46448600	Enhancers	Primary B cells from cord blood	blood
11	chr3:46446400-46448600	Enhancers	Placenta	Placenta
12	chr3:46446400-46448600	Enhancers	HUVEC	blood vessel
13	chr3:46446400-46448800	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:46446400-46448800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:46446600-46448600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr3:46446600-46448600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:46446800-46448600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:46446800-46448600	Enhancers	NHLF	lung
19	chr3:46446800-46449000	Enhancers	Pancreas	Pancrea
20	chr3:46446800-46450600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:46447000-46448600	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:46447000-46448600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:46447000-46448600	Enhancers	Gastric	stomach
24	chr3:46447000-46448600	Enhancers	NHDF-Ad	bronchial
25	chr3:46447200-46448600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:46447200-46448600	Enhancers	Fetal Stomach	stomach
27	chr3:46447200-46449800	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:46447800-46448600	Enhancers	Fetal Thymus	thymus
29	chr3:46447800-46448600	Enhancers	Small Intestine	intestine
30	chr3:46447800-46448600	Enhancers	GM12878-XiMat	blood
31	chr3:46447800-46448600	Enhancers	NH-A	brain
32	chr3:46447800-46449800	Active TSS	Rectal Smooth Muscle	rectum
33	chr3:46448000-46448600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr3:46448000-46448600	Flanking Active TSS	Colonic Mucosa	Colon
35	chr3:46448000-46448600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr3:46448000-46448600	Enhancers	Right Ventricle	heart
37	chr3:46448000-46449600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:46448000-46449800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:46448000-46450000	Enhancers	Brain Substantia Nigra	brain
40	chr3:46448000-46450000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr3:46448200-46448600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:46448200-46448600	Enhancers	Left Ventricle	heart
43	chr3:46448200-46448600	Flanking Active TSS	Stomach Mucosa	stomach
44	chr3:46448200-46448600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr3:46448200-46448800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:46448200-46448800	Enhancers	Brain Hippocampus Middle	brain
47	chr3:46448200-46448800	Flanking Active TSS	Lung	lung
48	chr3:46448200-46449400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:46448200-46449600	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr3:46448200-46449600	Flanking Active TSS	K562	blood

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