Variant report

Variant	rs28448438
Chromosome Location	chr4:56416665-56416666
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	TCF7L2	chr4:56415958-56416874	HCT-116	colon:	n/a	chr4:56416296-56416312 chr4:56416298-56416308 chr4:56416397-56416406 chr4:56416296-56416312 chr4:56416297-56416311
4	CEBPB	chr4:56415544-56416926	HCT-116	colon:	n/a	n/a
5	SRF	chr4:56415651-56416959	HCT-116	colon:	n/a	n/a
6	CEBPB	chr4:56415631-56416912	HCT-116	colon:	n/a	n/a
7	JUND	chr4:56415776-56417015	HCT-116	colon:	n/a	chr4:56416398-56416407 chr4:56416398-56416405
8	CBX3	chr4:56415692-56417223	HCT-116	colon:	n/a	n/a
9	CBX3	chr4:56415688-56416982	HCT-116	colon:	n/a	n/a
10	FOSL1	chr4:56415756-56416843	HCT-116	colon:	n/a	chr4:56416398-56416407 chr4:56416398-56416405
11	SP1	chr4:56415688-56417101	HCT-116	colon:	n/a	n/a
12	SP1	chr4:56415668-56416994	HCT-116	colon:	n/a	n/a
13	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: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10002541	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10005989	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10009593	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016506	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10026692	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10034433	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10462035	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133379	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11133382	0.86[EUR][1000 genomes]
rs11133383	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11133394	0.97[ASN][1000 genomes]
rs11133399	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726609	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733864	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11735267	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11931061	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11939815	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947476	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947623	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12646078	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13102385	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13121235	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13128582	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138697	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13152650	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522106	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1522107	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1522108	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1522110	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1522111	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17085889	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873092	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1965467	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980273	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130036	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2140077	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2177129	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412646	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412647	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412663	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28445925	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28463765	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28469692	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28514423	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28525309	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28572116	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28582059	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28670674	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28673496	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28713343	0.82[EUR][1000 genomes]
rs28790098	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899037	0.82[EUR][1000 genomes]
rs35767091	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736544	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736545	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3805147	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805152	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3805154	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805157	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817444	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828481	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4371676	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4580704	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs473005	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4864998	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865008	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59804446	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60797008	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60992571	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303714	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62309727	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554286	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554292	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810948	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6811520	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812042	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815516	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6817267	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6817663	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6819660	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824057	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6824955	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825994	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6829182	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6832769	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6834676	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6837710	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839788	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6846427	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6850524	0.97[ASN][1000 genomes]
rs6851838	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6853192	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs726967	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7660808	0.82[EUR][1000 genomes]
rs7667849	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7668147	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7670225	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7673908	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7677526	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7684810	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312662	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9684708	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9997288	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9998038	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998146	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56414000-56416800	Enhancers	Fetal Intestine Small	intestine
2	chr4:56414000-56419200	Weak transcription	Adipose Nuclei	Adipose
3	chr4:56414000-56419200	Weak transcription	Right Atrium	heart
4	chr4:56414000-56419400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:56414200-56417600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:56414200-56417600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:56414200-56420400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:56414400-56416800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:56414400-56417200	Enhancers	HMEC	breast
10	chr4:56414400-56417600	Enhancers	NHEK	skin
11	chr4:56414400-56418800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:56414400-56419000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:56414400-56419200	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:56414400-56419200	Weak transcription	GM12878-XiMat	blood
15	chr4:56414600-56416800	Enhancers	NHDF-Ad	bronchial
16	chr4:56414600-56416800	Enhancers	Osteobl	bone
17	chr4:56414600-56418200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:56414600-56419200	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:56414600-56419800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:56414800-56419000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:56414800-56419600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:56414800-56419600	Weak transcription	Fetal Lung	lung
23	chr4:56414800-56419800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:56414800-56419800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:56414800-56420000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:56414800-56420000	Weak transcription	Fetal Brain Female	brain
27	chr4:56415000-56419400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:56415000-56419600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:56415000-56419600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:56415000-56419800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:56415000-56419800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:56415000-56419800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:56415200-56419000	Weak transcription	HepG2	liver
34	chr4:56415600-56416800	Enhancers	HSMM	muscle
35	chr4:56415800-56416800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr4:56415800-56416800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:56415800-56416800	Enhancers	K562	blood
38	chr4:56416200-56416800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:56416400-56417000	Enhancers	NH-A	brain
40	chr4:56416400-56417600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:56416400-56419000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:56416400-56419200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:56416400-56419400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:56416400-56420600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:56416600-56416800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr4:56416600-56416800	Enhancers	Fetal Intestine Large	intestine
47	chr4:56416600-56419000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:56416600-56419200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:56416600-56419200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:56416600-56419200	Weak transcription	NHLF	lung

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