Variant report

Variant	rs11574441
Chromosome Location	chr3:46449175-46449176
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	MAX	chr3:46448047-46449447	K562	blood:	n/a	chr3:46448153-46448162
2	POLR2A	chr3:46448132-46450759	PBDE	blood:	n/a	n/a
3	POLR2A	chr3:46448373-46449180	GM12892	blood:	n/a	n/a
4	ZNF384	chr3:46448402-46449223	K562	blood:	n/a	n/a
5	RCOR1	chr3:46447943-46449285	K562	blood:	n/a	n/a
6	POLR2A	chr3:46448409-46449336	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:46447845-46449340	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr3:46447985-46449220	K562	blood:	n/a	chr3:46448153-46448162 chr3:46448021-46448031
9	NR2F2	chr3:46447587-46449528	K562	blood:	n/a	n/a
10	ARID3A	chr3:46448396-46449342	K562	blood:	n/a	n/a
11	POLR2A	chr3:46448504-46449238	U87	brain:	n/a	n/a
12	PML	chr3:46448300-46449223	K562	blood:	n/a	n/a
13	CUX1	chr3:46448117-46449422	K562	blood:	n/a	n/a
14	MAFF	chr3:46448443-46449284	K562	blood:	n/a	n/a
15	ZMIZ1	chr3:46447909-46449216	K562	blood:	n/a	n/a
16	ZNF143	chr3:46448462-46449320	K562	blood:	n/a	n/a
17	MYC	chr3:46448344-46449216	K562	blood:	n/a	n/a
18	MYC	chr3:46448362-46449191	K562	blood:	n/a	n/a
19	MTA3	chr3:46448217-46449195	GM12878	blood:	n/a	n/a
20	MAFK	chr3:46448378-46449341	K562	blood:	n/a	n/a
21	JUND	chr3:46447939-46449611	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
22	POLR2A	chr3:46448013-46449277	K562	blood:	n/a	n/a
23	CREB1	chr3:46448205-46449227	K562	blood:	n/a	n/a
24	TBP	chr3:46448405-46449188	K562	blood:	n/a	n/a
25	TRIM28	chr3:46448250-46449202	K562	blood:	n/a	n/a
26	ZC3H11A	chr3:46448048-46449224	K562	blood:	n/a	n/a
27	GATA2	chr3:46448019-46449181	HUVEC	blood vessel:	n/a	chr3:46448648-46448655
28	JUN	chr3:46448138-46449377	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
29	GATA1	chr3:46448307-46449913	PBDE	blood:	n/a	chr3:46448648-46448655
30	POLR2A	chr3:46448548-46449232	U87	brain:	n/a	n/a
31	EP300	chr3:46447985-46449392	K562	blood:	n/a	chr3:46448090-46448097 chr3:46448340-46448350
32	JUN	chr3:46447954-46449187	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
33	TAL1	chr3:46448140-46449351	K562	blood:	n/a	n/a
34	TEAD4	chr3:46448313-46449200	K562	blood:	n/a	n/a
35	NR2F2	chr3:46448003-46449198	K562	blood:	n/a	n/a
36	CEBPD	chr3:46448291-46449209	K562	blood:	n/a	n/a
37	POLR2A	chr3:46448315-46449200	HUVEC	blood vessel:	n/a	n/a
38	IRF1	chr3:46448405-46449272	K562	blood:	n/a	chr3:46449050-46449071
39	IRF1	chr3:46448538-46449220	K562	blood:	n/a	chr3:46449050-46449071
40	CBX3	chr3:46447982-46449253	K562	blood:	n/a	n/a
41	JUN	chr3:46447534-46450045	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
42	RCOR1	chr3:46447812-46449272	K562	blood:	n/a	n/a
43	TBL1XR1	chr3:46448131-46449187	K562	blood:	n/a	n/a
44	JUN	chr3:46448002-46449184	K562	blood:	n/a	chr3:46448150-46448161 chr3:46448153-46448164 chr3:46448607-46448616 chr3:46448154-46448163
45	POLR2A	chr3:46448306-46449308	K562	blood:	n/a	n/a
46	TEAD4	chr3:46447793-46449710	K562	blood:	n/a	n/a
47	MAX	chr3:46448330-46449183	NB4	blood:	n/a	n/a
48	UBTF	chr3:46448071-46449207	K562	blood:	n/a	n/a
49	IRF1	chr3:46448382-46449542	K562	blood:	n/a	chr3:46449459-46449469 chr3:46449050-46449071 chr3:46449459-46449473
50	ELF1	chr3:46448321-46449185	K562	blood:	n/a	chr3:46448732-46448743

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-CCR5-1	chr3:46448880-46449453	NONHSAT089438

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

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11574431	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574439	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11574440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575814	1.00[EUR][1000 genomes]
rs11575817	1.00[EUR][1000 genomes]
rs11575818	1.00[EUR][1000 genomes]
rs11575822	1.00[EUR][1000 genomes]
rs13327723	1.00[EUR][1000 genomes]
rs17141003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17141076	1.00[EUR][1000 genomes]
rs17842821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17842822	1.00[EUR][1000 genomes]
rs2373253	1.00[EUR][1000 genomes]
rs3136536	1.00[EUR][1000 genomes]
rs3176763	1.00[EUR][1000 genomes]
rs3181037	1.00[EUR][1000 genomes]
rs35212534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3918370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41495153	1.00[EUR][1000 genomes]
rs55951695	1.00[EUR][1000 genomes]
rs56062522	1.00[EUR][1000 genomes]
rs57509359	1.00[EUR][1000 genomes]
rs57761566	1.00[EUR][1000 genomes]
rs58966767	1.00[EUR][1000 genomes]
rs59998539	1.00[EUR][1000 genomes]
rs60350631	1.00[EUR][1000 genomes]
rs61737000	1.00[EUR][1000 genomes]
rs6441969	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770833	1.00[EUR][1000 genomes]
rs6776013	0.97[AFR][1000 genomes]
rs6798819	1.00[EUR][1000 genomes]
rs6801203	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs723577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831107	1.00[EUR][1000 genomes]
rs7611447	1.00[EUR][1000 genomes]
rs7614209	1.00[EUR][1000 genomes]
rs7638702	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640708	1.00[EUR][1000 genomes]
rs7650273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652954	1.00[EUR][1000 genomes]
rs9282632	1.00[EUR][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:80 , 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	chr3:46446800-46450600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:46447200-46449800	Enhancers	Fetal Muscle Trunk	muscle
6	chr3:46447800-46449800	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:46448000-46449600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:46448000-46449800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:46448000-46450000	Enhancers	Brain Substantia Nigra	brain
10	chr3:46448000-46450000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr3:46448200-46449400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:46448200-46449600	Flanking Active TSS	Fetal Intestine Large	intestine
13	chr3:46448200-46449600	Flanking Active TSS	K562	blood
14	chr3:46448200-46449800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:46448200-46449800	Flanking Active TSS	Hela-S3	cervix
16	chr3:46448200-46450200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:46448200-46452000	Enhancers	Dnd41	blood
18	chr3:46448400-46449200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr3:46448400-46449200	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:46448400-46449400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr3:46448400-46449600	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr3:46448400-46449800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr3:46448400-46449800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:46448400-46450000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:46448400-46450000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:46448400-46450000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:46448400-46450200	Flanking Active TSS	HSMM	muscle
28	chr3:46448400-46450200	Flanking Active TSS	Osteobl	bone
29	chr3:46448400-46450400	Enhancers	Fetal Heart	heart
30	chr3:46448600-46449200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:46448600-46449200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr3:46448600-46449200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr3:46448600-46449200	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr3:46448600-46449200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:46448600-46449200	Flanking Active TSS	Placenta	Placenta
36	chr3:46448600-46449200	Active TSS	Thymus	Thymus
37	chr3:46448600-46449400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr3:46448600-46449400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:46448600-46449400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr3:46448600-46449400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr3:46448600-46449400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:46448600-46449400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:46448600-46449400	Flanking Active TSS	Fetal Stomach	stomach
44	chr3:46448600-46449400	Active TSS	Left Ventricle	heart
45	chr3:46448600-46449400	Active TSS	Right Ventricle	heart
46	chr3:46448600-46449400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr3:46448600-46449400	Active TSS	Small Intestine	intestine
48	chr3:46448600-46449400	Active TSS	Stomach Mucosa	stomach
49	chr3:46448600-46449400	Flanking Active TSS	GM12878-XiMat	blood
50	chr3:46448600-46449400	Flanking Active TSS	NH-A	brain

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