Variant report

Variant	rs6554287
Chromosome Location	chr4:56416879-56416880
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	SIN3AK20	chr4:56415524-56416960	HCT-116	colon:	n/a	n/a
2	JUND	chr4:56415659-56416979	HCT-116	colon:	n/a	chr4:56416398-56416407 chr4:56416398-56416405
3	CEBPB	chr4:56415544-56416926	HCT-116	colon:	n/a	n/a
4	SRF	chr4:56415651-56416959	HCT-116	colon:	n/a	n/a
5	CEBPB	chr4:56415631-56416912	HCT-116	colon:	n/a	n/a
6	JUND	chr4:56415776-56417015	HCT-116	colon:	n/a	chr4:56416398-56416407 chr4:56416398-56416405
7	CBX3	chr4:56415692-56417223	HCT-116	colon:	n/a	n/a
8	CBX3	chr4:56415688-56416982	HCT-116	colon:	n/a	n/a
9	SP1	chr4:56415688-56417101	HCT-116	colon:	n/a	n/a
10	SP1	chr4:56415668-56416994	HCT-116	colon:	n/a	n/a
11	FOSL1	chr4:56415752-56416940	HCT-116	colon:	n/a	chr4:56416398-56416407 chr4:56416398-56416405

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56415018..56417689-chr4:56438366..56440978,2	MCF-7	breast:
2	chr4:56410648..56414304-chr4:56416638..56420885,5	MCF-7	breast:

Variant related genes	Relation type
CLOCK	TF binding region
ENSG00000272969	Chromatin interaction
ENSG00000134852	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10012559	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10034170	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1021306	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1021307	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10462033	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1048004	0.86[EUR][1000 genomes]
rs10529258	0.85[EUR][1000 genomes]
rs10866424	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11240	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11732481	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11939971	0.84[EUR][1000 genomes]
rs12505265	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12509047	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13133077	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13134079	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1488941	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1522109	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546004	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17721215	0.87[EUR][1000 genomes]
rs17721497	0.84[EUR][1000 genomes]
rs17722870	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17722979	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17779627	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1801260	0.86[EUR][1000 genomes]
rs1906676	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1967078	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979604	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1979605	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2070062	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2101476	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2130038	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2130040	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2412658	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2412659	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2412661	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2412662	0.84[EUR][1000 genomes]
rs3805156	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41324951	0.86[EUR][1000 genomes]
rs4336288	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4865006	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4865012	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865014	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55729020	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55869433	0.83[ASN][1000 genomes]
rs55885973	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56056791	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56152424	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56196624	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57338268	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58476959	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303686	0.86[EUR][1000 genomes]
rs62303691	0.87[EUR][1000 genomes]
rs62303692	0.86[EUR][1000 genomes]
rs62303708	0.87[EUR][1000 genomes]
rs62303711	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62303712	0.92[EUR][1000 genomes]
rs62303713	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62303715	0.80[ASN][1000 genomes]
rs62303716	0.80[ASN][1000 genomes]
rs62303718	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62303722	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62303724	0.80[ASN][1000 genomes]
rs62303726	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303728	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303730	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303731	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303732	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305264	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305265	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305266	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62305267	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305268	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305269	0.83[ASN][1000 genomes]
rs62305270	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62305271	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62309728	0.83[ASN][1000 genomes]
rs62309729	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62309730	0.83[ASN][1000 genomes]
rs62309758	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309759	0.88[ASN][1000 genomes]
rs62310862	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62310866	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6554282	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554283	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554284	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6554285	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554290	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554291	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67963898	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6802	0.86[EUR][1000 genomes]
rs6822553	0.90[EUR][1000 genomes]
rs6828474	0.80[ASN][1000 genomes]
rs6830728	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6846764	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6848755	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6851971	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6853506	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6856004	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs716806	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236140	0.86[EUR][1000 genomes]
rs73236142	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73236149	0.83[ASN][1000 genomes]
rs73236153	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7659095	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7660668	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7665286	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7665846	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7676245	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7681414	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7683997	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7697067	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7698022	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs972446	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9993599	0.88[AMR][1000 genomes];0.93[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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56414000-56419200	Weak transcription	Adipose Nuclei	Adipose
2	chr4:56414000-56419200	Weak transcription	Right Atrium	heart
3	chr4:56414000-56419400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:56414200-56417600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:56414200-56417600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:56414200-56420400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:56414400-56417200	Enhancers	HMEC	breast
8	chr4:56414400-56417600	Enhancers	NHEK	skin
9	chr4:56414400-56418800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:56414400-56419000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:56414400-56419200	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:56414400-56419200	Weak transcription	GM12878-XiMat	blood
13	chr4:56414600-56418200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:56414600-56419200	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:56414600-56419800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:56414800-56419000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:56414800-56419600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:56414800-56419600	Weak transcription	Fetal Lung	lung
19	chr4:56414800-56419800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:56414800-56419800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr4:56414800-56420000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:56414800-56420000	Weak transcription	Fetal Brain Female	brain
23	chr4:56415000-56419400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:56415000-56419600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:56415000-56419600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:56415000-56419800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:56415000-56419800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:56415000-56419800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:56415200-56419000	Weak transcription	HepG2	liver
30	chr4:56416400-56417000	Enhancers	NH-A	brain
31	chr4:56416400-56417600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:56416400-56419000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:56416400-56419200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:56416400-56419400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:56416400-56420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:56416600-56419000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:56416600-56419200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:56416600-56419200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:56416600-56419200	Weak transcription	NHLF	lung
40	chr4:56416800-56419000	Weak transcription	Osteobl	bone
41	chr4:56416800-56419400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:56416800-56419400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:56416800-56419400	Weak transcription	HSMM	muscle
44	chr4:56416800-56419400	Weak transcription	NHDF-Ad	bronchial
45	chr4:56416800-56420600	Weak transcription	Fetal Intestine Large	intestine
46	chr4:56416800-56425600	Weak transcription	K562	blood

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