Variant report

Variant	rs6450034
Chromosome Location	chr5:68627806-68627807
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr5:68627737-68628099	T-47D	breast:	n/a	n/a
2	MAX	chr5:68627739-68628939	NB4	blood:	n/a	chr5:68628650-68628661 chr5:68628659-68628666 chr5:68628651-68628660 chr5:68628661-68628670 chr5:68628651-68628660 chr5:68628649-68628662 chr5:68628651-68628660
3	HNF4G	chr5:68627649-68628040	HepG2	liver:	n/a	n/a
4	FOXA1	chr5:68627709-68628034	T-47D	breast:	n/a	n/a
5	POLR2A	chr5:68627479-68628844	HepG2	liver:	n/a	n/a
6	RCOR1	chr5:68627735-68628862	HepG2	liver:	n/a	n/a
7	ARID3A	chr5:68627607-68628919	HepG2	liver:	n/a	n/a
8	HNF4A	chr5:68627720-68627983	HepG2	liver:	n/a	n/a
9	RFX5	chr5:68627743-68627957	HepG2	liver:	n/a	n/a
10	USF2	chr5:68627791-68627971	HepG2	liver:	n/a	n/a
11	MYBL2	chr5:68627533-68628258	HepG2	liver:	n/a	n/a
12	SMC3	chr5:68627545-68628044	HepG2	liver:	n/a	n/a
13	HEY1	chr5:68627333-68628141	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:68627608-68628920	GM12878	blood:	n/a	n/a
15	CHD2	chr5:68627744-68628014	HepG2	liver:	n/a	n/a
16	TBP	chr5:68627466-68628129	HepG2	liver:	n/a	n/a
17	ZNF263	chr5:68627408-68627907	HEK293-T-REx	kidney:	n/a	chr5:68627520-68627529
18	POLR2A	chr5:68627305-68628118	HepG2	liver:	n/a	n/a
19	FOXA1	chr5:68627611-68628034	HepG2	liver:	n/a	n/a
20	POLR2A	chr5:68627653-68628960	GM12891	blood:	n/a	n/a
21	FOXA1	chr5:68627712-68628162	HepG2	liver:	n/a	n/a
22	NFIC	chr5:68627641-68628071	HepG2	liver:	n/a	n/a
23	MXI1	chr5:68627542-68628106	HepG2	liver:	n/a	n/a
24	FOXA1	chr5:68627598-68628205	HepG2	liver:	n/a	n/a
25	HCFC1	chr5:68627600-68629135	Hela-S3	cervix:	n/a	n/a
26	FOXA1	chr5:68627681-68628132	HepG2	liver:	n/a	n/a
27	EP300	chr5:68627600-68628124	HepG2	liver:	n/a	n/a
28	ELF1	chr5:68627366-68627919	HepG2	liver:	n/a	n/a
29	MYBL2	chr5:68627423-68628186	HepG2	liver:	n/a	n/a
30	EP300	chr5:68627802-68628842	HepG2	liver:	n/a	n/a
31	FOXA2	chr5:68627687-68628099	HepG2	liver:	n/a	n/a
32	TEAD4	chr5:68627399-68628231	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:68627768-68628048	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:68627764-68628017	HepG2	liver:	n/a	n/a
35	HEY1	chr5:68627766-68628183	HepG2	liver:	n/a	n/a
36	HDAC2	chr5:68627753-68628051	HepG2	liver:	n/a	n/a
37	POLR2A	chr5:68627441-68628937	HepG2	liver:	n/a	n/a
38	NRF1	chr5:68627726-68628919	SK-N-SH	brain:	n/a	chr5:68628614-68628625 chr5:68628611-68628625 chr5:68628614-68628625
39	POLR2A	chr5:68626982-68628073	MCF-7	breast:	n/a	n/a
40	HNF4A	chr5:68627652-68628042	HepG2	liver:	n/a	n/a
41	POLR2A	chr5:68627741-68628026	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
2	chr5:68626762..68628383-chr5:68787111..68789288,2	MCF-7	breast:
3	chr5:68485299..68487066-chr5:68626120..68629033,4	MCF-7	breast:
4	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
5	chr5:68606839..68610803-chr5:68625940..68628885,4	MCF-7	breast:
6	chr5:68529975..68532202-chr5:68627120..68629377,3	MCF-7	breast:
7	chr5:68588146..68590724-chr5:68626782..68628489,2	MCF-7	breast:
8	chr5:68626208..68627882-chr5:68665634..68668081,2	MCF-7	breast:
9	chr5:68511595..68514121-chr5:68626401..68628217,2	MCF-7	breast:
10	chr5:68534808..68537076-chr5:68626446..68628069,2	MCF-7	breast:
11	chr5:68388706..68391393-chr5:68627238..68631529,6	MCF-7	breast:

No data

Variant related genes	Relation type
CHCHD2P2	TF binding region
ENSG00000153044	Chromatin interaction
ENSG00000197822	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000213830	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28485298	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28493733	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28513857	0.85[EUR][1000 genomes]
rs28584613	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56315603	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7728611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
2	chr5:68609800-68628200	Weak transcription	Right Ventricle	heart
3	chr5:68609800-68628400	Weak transcription	Lung	lung
4	chr5:68611000-68628200	Weak transcription	Aorta	Aorta
5	chr5:68616600-68628200	Weak transcription	Left Ventricle	heart
6	chr5:68621000-68628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:68627000-68628800	Active TSS	Duodenum Mucosa	Duodenum
8	chr5:68627200-68628000	Active TSS	Rectal Smooth Muscle	rectum
9	chr5:68627200-68628400	Weak transcription	Gastric	stomach
10	chr5:68627200-68628800	Active TSS	Colonic Mucosa	Colon
11	chr5:68627200-68629200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr5:68627400-68628000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr5:68627400-68628000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:68627400-68628000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:68627400-68628000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:68627400-68628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:68627400-68628200	Enhancers	Spleen	Spleen
18	chr5:68627400-68628200	Flanking Active TSS	Hela-S3	cervix
19	chr5:68627400-68628400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:68627400-68628800	Active TSS	Fetal Intestine Small	intestine
21	chr5:68627400-68628800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:68627400-68628800	Active TSS	Fetal Stomach	stomach
23	chr5:68627400-68628800	Flanking Active TSS	HMEC	breast
24	chr5:68627400-68629000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr5:68627400-68629000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr5:68627400-68629000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr5:68627400-68629000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr5:68627400-68629000	Flanking Active TSS	NHEK	skin
29	chr5:68627400-68629200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:68627600-68628000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:68627600-68628000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr5:68627600-68628000	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr5:68627600-68628000	Enhancers	Brain Anterior Caudate	brain
34	chr5:68627600-68628000	Enhancers	Brain Substantia Nigra	brain
35	chr5:68627600-68628000	Enhancers	Fetal Heart	heart
36	chr5:68627600-68628000	Flanking Active TSS	Placenta	Placenta
37	chr5:68627600-68628000	Flanking Active TSS	A549	lung
38	chr5:68627600-68628000	Flanking Active TSS	K562	blood
39	chr5:68627600-68628200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:68627600-68628200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:68627600-68628200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:68627600-68628200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr5:68627600-68628200	Weak transcription	Esophagus	oesophagus
44	chr5:68627600-68628200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr5:68627600-68628200	Flanking Active TSS	Dnd41	blood
46	chr5:68627600-68628400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr5:68627600-68628400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:68627600-68628400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr5:68627600-68628400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr5:68627600-68628400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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