Variant report

Variant	rs28521883
Chromosome Location	chr5:95297668-95297669
allele	C/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	NFIC	chr5:95297595-95297932	HepG2	liver:	n/a	n/a
2	CTCF	chr5:95297656-95298232	K562	blood:	n/a	n/a
3	NFYB	chr5:95297532-95298014	GM12878	blood:	n/a	n/a
4	ATF2	chr5:95297535-95298585	H1-hESC	embryonic stem cell:	n/a	chr5:95297746-95297760 chr5:95297782-95297793
5	NR3C1	chr5:95297593-95297972	A549	lung:	n/a	n/a
6	MYC	chr5:95296370-95298804	K562	blood:	n/a	n/a
7	MXI1	chr5:95295550-95298162	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:95297169-95297701	U87	brain:	n/a	n/a
9	RAD21	chr5:95295552-95298217	IMR90	lung:	n/a	chr5:95296846-95296859 chr5:95297062-95297075 chr5:95296847-95296861 chr5:95297059-95297078
10	CEBPB	chr5:95297608-95297919	Hela-S3	cervix:	n/a	n/a
11	NR3C1	chr5:95297605-95298183	A549	lung:	n/a	n/a
12	POLR2A	chr5:95294827-95298308	GM12892	blood:	n/a	n/a
13	RELA	chr5:95294993-95298352	GM12891	blood:	n/a	chr5:95297005-95297014 chr5:95297005-95297014
14	NFIC	chr5:95297471-95298149	GM12878	blood:	n/a	n/a
15	SRF	chr5:95297619-95298166	ECC-1	luminal epithelium:	n/a	chr5:95298010-95298027 chr5:95298007-95298025 chr5:95298009-95298020 chr5:95298010-95298021 chr5:95298007-95298024 chr5:95298010-95298024 chr5:95298011-95298022 chr5:95298009-95298022 chr5:95298011-95298020 chr5:95298008-95298023 chr5:95298007-95298021 chr5:95298005-95298023 chr5:95298011-95298025
16	POLR2A	chr5:95296365-95297919	MCF-7	breast:	n/a	n/a
17	BHLHE40	chr5:95297630-95298297	HepG2	liver:	n/a	n/a
18	TBP	chr5:95297235-95298284	GM12878	blood:	n/a	n/a
19	CHD1	chr5:95295706-95298302	GM12878	blood:	n/a	chr5:95296574-95296584
20	TAF1	chr5:95296878-95298250	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr5:95297631-95298917	K562	blood:	n/a	chr5:95298844-95298858
22	POLR2A	chr5:95297206-95297766	PFSK-1	brain:	n/a	n/a
23	JUN	chr5:95297610-95297946	HUVEC	blood vessel:	n/a	chr5:95297782-95297795 chr5:95297783-95297792 chr5:95297631-95297640
24	POLR2A	chr5:95296312-95297766	H1-neurons	neurons:	n/a	n/a
25	PML	chr5:95295247-95298289	GM12878	blood:	n/a	chr5:95296249-95296257
26	POLR2A	chr5:95297180-95297679	HepG2	liver:	n/a	n/a
27	E2F4	chr5:95296295-95298203	K562	blood:	n/a	chr5:95297782-95297791 chr5:95297687-95297696 chr5:95297196-95297206 chr5:95297784-95297793 chr5:95297056-95297065
28	SP4	chr5:95297437-95298271	H1-hESC	embryonic stem cell:	n/a	chr5:95297682-95297698 chr5:95297893-95297909
29	POLR2A	chr5:95294744-95298231	GM12891	blood:	n/a	n/a
30	ZC3H11A	chr5:95297635-95298226	K562	blood:	n/a	n/a
31	YY1	chr5:95296880-95297746	H1-hESC	embryonic stem cell:	n/a	chr5:95297190-95297204 chr5:95297056-95297065 chr5:95297199-95297213 chr5:95297054-95297068 chr5:95297018-95297029
32	CREB1	chr5:95297453-95298256	ECC-1	luminal epithelium:	n/a	chr5:95297781-95297794
33	POLR2A	chr5:95294626-95298807	GM12892	blood:	n/a	n/a
34	POLR2A	chr5:95296592-95298135	HepG2	liver:	n/a	n/a
35	POLR2A	chr5:95294626-95298519	GM12892	blood:	n/a	n/a
36	CCNT2	chr5:95296387-95298017	K562	blood:	n/a	chr5:95297897-95297906 chr5:95296574-95296583
37	POLR2A	chr5:95295651-95298283	GM18951	blood:	n/a	n/a
38	MXI1	chr5:95297587-95297913	Hela-S3	cervix:	n/a	n/a
39	ELF1	chr5:95296188-95298180	GM12878	blood:	n/a	chr5:95297194-95297206
40	JUND	chr5:95297581-95298814	H1-hESC	embryonic stem cell:	n/a	chr5:95297783-95297792 chr5:95297631-95297640
41	NFYB	chr5:95297503-95298017	K562	blood:	n/a	n/a
42	FOXP2	chr5:95296895-95298168	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr5:95296810-95298306	K562	blood:	n/a	n/a
44	POLR2A	chr5:95297139-95297876	U87	brain:	n/a	n/a
45	POLR2A	chr5:95296853-95298273	K562	blood:	n/a	n/a
46	POLR2A	chr5:95293827-95297878	ProgFib	skin:	n/a	n/a
47	NR3C1	chr5:95297489-95298239	A549	lung:	n/a	n/a
48	POLR2A	chr5:95294579-95298340	GM12878	blood:	n/a	n/a
49	NR3C1	chr5:95297418-95298240	A549	lung:	n/a	n/a
50	CREB1	chr5:95296849-95298784	K562	blood:	n/a	chr5:95297781-95297794

No.	Distal block	Cell Line	Cell type
1	chr15:65588296..65588838-chr5:95297026..95297696,2	Hela-S3	cervix:
2	chr5:94979878..94983810-chr5:95295717..95298674,4	K562	blood:
3	chr5:95296142..95297757-chr5:95548308..95551059,2	MCF-7	breast:
4	chr15:65321247..65322203-chr5:95297173..95297723,2	NB4	blood:
5	chr5:95294835..95302887-chr5:95306601..95313873,11	K562	blood:
6	chr5:95295795..95298001-chr5:95305862..95309802,3	MCF-7	breast:
7	chr5:95297276..95297777-chr9:88714838..88715592,2	HCT-116	colon:
8	chr5:95195786..95198605-chr5:95296132..95297926,2	MCF-7	breast:
9	chr5:94981287..94984175-chr5:95296229..95298674,3	K562	blood:

Variant related genes	Relation type
ELL2	TF binding region
ENSG00000251314	TF binding region
ENSG00000103707	Chromatin interaction
ENSG00000249746	Chromatin interaction
ENSG00000213716	Chromatin interaction
ENSG00000250362	Chromatin interaction
ENSG00000135052	Chromatin interaction
ENSG00000175449	Chromatin interaction
ENSG00000199568	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10428657	1.00[EUR][1000 genomes]
rs10428702	1.00[EUR][1000 genomes]
rs10515233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515234	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948037	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12514472	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12514954	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12517786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523306	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085220	1.00[EUR][1000 genomes]
rs17085223	1.00[EUR][1000 genomes]
rs17085224	1.00[EUR][1000 genomes]
rs17085227	1.00[EUR][1000 genomes]
rs17085243	1.00[EUR][1000 genomes]
rs17085339	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17085366	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085373	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085393	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085426	1.00[EUR][1000 genomes]
rs3756701	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777174	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3777176	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777177	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777180	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41276261	1.00[EUR][1000 genomes]
rs55763081	1.00[EUR][1000 genomes]
rs56776515	1.00[EUR][1000 genomes]
rs58389685	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60908902	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61268106	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6143071	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6556897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861075	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870388	1.00[EUR][1000 genomes]
rs6872006	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874371	1.00[EUR][1000 genomes]
rs6891082	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891633	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893788	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73771827	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700606	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724475	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736480	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9687631	1.00[EUR][1000 genomes]
rs977128	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977129	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv3388808	chr5:95296221-95299069	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 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	chr5:95293800-95297800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr5:95294000-95298000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:95294000-95298000	Active TSS	Rectal Smooth Muscle	rectum
4	chr5:95294400-95297800	Active TSS	HSMMtube	muscle
5	chr5:95294400-95298600	Active TSS	Aorta	Aorta
6	chr5:95294600-95298000	Active TSS	Brain Angular Gyrus	brain
7	chr5:95294600-95298200	Active TSS	Fetal Intestine Large	intestine
8	chr5:95294600-95298200	Active TSS	GM12878-XiMat	blood
9	chr5:95294600-95298400	Active TSS	Brain Substantia Nigra	brain
10	chr5:95295000-95298000	Active TSS	Gastric	stomach
11	chr5:95295000-95298400	Active TSS	Colonic Mucosa	Colon
12	chr5:95295000-95298600	Active TSS	Brain Hippocampus Middle	brain
13	chr5:95295200-95298200	Active TSS	Small Intestine	intestine
14	chr5:95295400-95298200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:95295400-95298200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr5:95295400-95298200	Active TSS	Brain Anterior Caudate	brain
17	chr5:95295400-95298400	Active TSS	Pancreas	Pancrea
18	chr5:95295400-95298600	Active TSS	Right Ventricle	heart
19	chr5:95295600-95297800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:95295600-95297800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:95295600-95297800	Active TSS	Hela-S3	cervix
22	chr5:95295600-95298000	Active TSS	Liver	Liver
23	chr5:95295600-95298000	Active TSS	Fetal Heart	heart
24	chr5:95295600-95298200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:95295600-95298200	Active TSS	Lung	lung
26	chr5:95295600-95298200	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr5:95295600-95298200	Active TSS	NHDF-Ad	bronchial
28	chr5:95295600-95298400	Active TSS	Left Ventricle	heart
29	chr5:95295600-95298400	Active TSS	Right Atrium	heart
30	chr5:95295600-95298600	Active TSS	Brain Cingulate Gyrus	brain
31	chr5:95295600-95298800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr5:95295800-95298000	Active TSS	A549	lung
33	chr5:95295800-95298200	Active TSS	Colon Smooth Muscle	Colon
34	chr5:95295800-95298200	Active TSS	Esophagus	oesophagus
35	chr5:95295800-95298200	Active TSS	Psoas Muscle	Psoas
36	chr5:95295800-95298400	Active TSS	Ovary	ovary
37	chr5:95295800-95298400	Active TSS	Osteobl	bone
38	chr5:95295800-95298600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:95295800-95298600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr5:95296000-95297800	Active TSS	NH-A	brain
41	chr5:95296000-95298200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:95296000-95298200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:95296000-95298200	Active TSS	Stomach Mucosa	stomach
44	chr5:95296000-95298200	Active TSS	HSMM	muscle
45	chr5:95296200-95297800	Active TSS	Placenta	Placenta
46	chr5:95296200-95298000	Active TSS	Fetal Brain Female	brain
47	chr5:95296200-95298000	Active TSS	HMEC	breast
48	chr5:95296200-95298000	Active TSS	HUVEC	blood vessel
49	chr5:95296200-95298200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:95296200-95298200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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