Variant report

Variant	rs13133608
Chromosome Location	chr4:90032048-90032049
allele	C/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	POLR2A	chr4:90032026-90033501	GM18505	blood:	n/a	n/a
2	POLR2A	chr4:90031952-90033122	GM18526	blood:	n/a	n/a
3	MAX	chr4:90031662-90033107	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
4	SIN3AK20	chr4:90031811-90033148	MCF-7	breast:	n/a	n/a
5	GABPA	chr4:90031608-90032150	H1-hESC	embryonic stem cell:	n/a	n/a
6	BHLHE40	chr4:90032021-90033369	GM12878	blood:	n/a	chr4:90032093-90032109
7	SETDB1	chr4:90031866-90033084	K562	blood:	n/a	n/a
8	FOXA2	chr4:90032023-90032732	A549	lung:	n/a	n/a
9	POLR2A	chr4:90032026-90032528	GM12878	blood:	n/a	n/a
10	MXI1	chr4:90031599-90033231	GM12878	blood:	n/a	chr4:90031789-90031804
11	MAX	chr4:90031818-90033188	HepG2	liver:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
12	POLR2A	chr4:90031925-90033139	GM19193	blood:	n/a	n/a
13	RELA	chr4:90031877-90033556	GM10847	blood:	n/a	n/a
14	BHLHE40	chr4:90031774-90033235	K562	blood:	n/a	chr4:90032093-90032109 chr4:90031987-90032003
15	MAX	chr4:90031702-90033805	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
16	EBF1	chr4:90031991-90032947	GM12878	blood:	n/a	chr4:90032399-90032410
17	CBX3	chr4:90031993-90033181	K562	blood:	n/a	n/a
18	CTCF	chr4:90032033-90032804	K562	blood:	n/a	n/a
19	EP300	chr4:90031929-90033121	ECC-1	luminal epithelium:	n/a	chr4:90032597-90032613
20	POLR2A	chr4:90031741-90033492	GM19099	blood:	n/a	n/a
21	E2F4	chr4:90031914-90033095	K562	blood:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
22	E2F6	chr4:90031734-90033155	H1-hESC	embryonic stem cell:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
23	SIN3AK20	chr4:90032033-90032988	K562	blood:	n/a	n/a
24	POLR2A	chr4:90031758-90033089	MCF-7	breast:	n/a	n/a
25	YY1	chr4:90032005-90033062	HepG2	liver:	n/a	chr4:90032571-90032582 chr4:90032633-90032642 chr4:90032631-90032645
26	E2F6	chr4:90031686-90033217	H1-hESC	embryonic stem cell:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
27	CHD1	chr4:90031786-90033305	GM12878	blood:	n/a	n/a
28	FOXA1	chr4:90031979-90032911	HepG2	liver:	n/a	n/a
29	MYC	chr4:90031682-90032925	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
30	USF2	chr4:90032047-90032223	H1-hESC	embryonic stem cell:	n/a	chr4:90032093-90032109
31	RCOR1	chr4:90031590-90032995	GM12878	blood:	n/a	n/a
32	MAX	chr4:90032018-90033051	HepG2	liver:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
33	UBTF	chr4:90031882-90033927	K562	blood:	n/a	n/a
34	MTA3	chr4:90032028-90032567	GM12878	blood:	n/a	n/a
35	MYC	chr4:90031728-90033645	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
36	MXI1	chr4:90031723-90034038	HepG2	liver:	n/a	chr4:90031789-90031804
37	CCNT2	chr4:90031987-90033323	K562	blood:	n/a	chr4:90032568-90032577 chr4:90032597-90032606 chr4:90032633-90032642
38	STAT1	chr4:90032046-90032866	GM12878	blood:	n/a	chr4:90032568-90032580
39	CTCF	chr4:90032036-90032743	MCF-7	breast:	n/a	n/a
40	MAX	chr4:90031865-90033151	GM12878	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
41	MAX	chr4:90032025-90033085	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
42	ARID3A	chr4:90031746-90032396	HepG2	liver:	n/a	n/a
43	USF2	chr4:90031770-90032744	GM12878	blood:	n/a	chr4:90032093-90032109 chr4:90031987-90032003
44	BACH1	chr4:90031960-90032541	K562	blood:	n/a	n/a
45	ELF1	chr4:90032041-90033004	K562	blood:	n/a	n/a
46	TCF3	chr4:90031918-90032960	GM12878	blood:	n/a	n/a
47	MAX	chr4:90031902-90032978	MCF-7	breast:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
48	POLR2A	chr4:90031750-90033337	GM12878	blood:	n/a	n/a
49	POLR2A	chr4:90031965-90032053	Gliobla	brain:	n/a	n/a
50	MAX	chr4:90031663-90033047	H1-hESC	embryonic stem cell:	n/a	chr4:90032609-90032618 chr4:90032634-90032644

No.	Distal block	Cell Line	Cell type
1	chr4:89739936..89740488-chr4:90031811..90032510,2	MCF-7	breast:
2	chr4:89443831..89446134-chr4:90031080..90033028,2	K562	blood:
3	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:
4	chr4:89739661..89740284-chr4:90031824..90032453,2	MCF-7	breast:
5	chr4:90021012..90023295-chr4:90030744..90032396,2	K562	blood:
6	chr4:90030188..90033002-chr4:90049823..90052502,2	MCF-7	breast:

Variant related genes	Relation type
TIGD2	TF binding region
ENSG00000271359	TF binding region
ENSG00000138641	Chromatin interaction
ENSG00000145337	Chromatin interaction
ENSG00000212226	Chromatin interaction
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10001420	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10433881	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734924	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645173	0.96[ASN][1000 genomes]
rs12647095	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649875	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105546	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138927	0.96[ASN][1000 genomes]
rs1355836	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1355837	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398937	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398938	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398939	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398941	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398943	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513811	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513812	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513823	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533288	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533289	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533294	0.96[ASN][1000 genomes]
rs1708659	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1708671	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1708672	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1708673	0.81[ASN][1000 genomes]
rs1708683	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1795730	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1795735	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1795737	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1795740	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1828735	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1996139	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2056013	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2102650	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464511	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670618	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2670619	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670620	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670627	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2670628	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2704580	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704585	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2704592	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28559811	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2869989	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28718401	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28869547	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2904264	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4325981	0.96[ASN][1000 genomes]
rs4693219	0.88[AMR][1000 genomes]
rs4693984	0.86[AMR][1000 genomes]
rs4693987	0.96[ASN][1000 genomes]
rs6532100	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6532113	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823241	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826482	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6834297	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6843986	0.86[ASN][1000 genomes]
rs6845264	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846010	0.92[ASN][1000 genomes]
rs7657630	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180333	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9307063	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938265	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs938267	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999793	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9999873	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3437234	chr4:90031454-90034302	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90030800-90033600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:90031000-90033400	Active TSS	Pancreas	Pancrea
3	chr4:90031200-90033000	Active TSS	Fetal Brain Female	brain
4	chr4:90031200-90033200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:90031200-90033400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:90031400-90032200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
7	chr4:90031400-90032200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr4:90031400-90032200	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr4:90031400-90032200	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr4:90031400-90032200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr4:90031400-90032400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:90031400-90032400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr4:90031400-90032400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
14	chr4:90031400-90033400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr4:90031400-90033400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr4:90031400-90033600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:90031600-90032200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:90031600-90032200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr4:90031600-90032200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
25	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:90031600-90032200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr4:90031600-90032200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Thymus	Thymus
33	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	HMEC	breast
34	chr4:90031600-90032200	Bivalent/Poised TSS	HSMMtube	muscle
35	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
36	chr4:90031600-90032200	Flanking Bivalent TSS/Enh	Osteobl	bone
37	chr4:90031600-90032400	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
39	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr4:90031600-90032400	Flanking Active TSS	Placenta	Placenta
42	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr4:90031600-90033200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr4:90031600-90033200	Active TSS	Brain Substantia Nigra	brain
46	chr4:90031600-90033200	Active TSS	Fetal Intestine Small	intestine
47	chr4:90031600-90033400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr4:90031600-90033400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:90031600-90033400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr4:90031600-90033400	Active TSS	Right Atrium	heart

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