Variant report

Variant	rs6601067
Chromosome Location	chr5:179129875-179129876
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179129453-179130751	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:179129511-179130077	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:179129326-179129897	PANC-1	pancreas:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179127758..179131964-chr5:179232228..179234815,3	MCF-7	breast:
2	chr5:179102777..179105502-chr5:179129566..179131277,2	MCF-7	breast:
3	chr5:179129685..179132691-chr5:179151182..179153644,5	K562	blood:
4	chr5:179128478..179132558-chr5:179135787..179140840,4	MCF-7	breast:
5	chr5:179127269..179130217-chr5:179212553..179215180,2	K562	blood:
6	chr5:179129274..179131035-chr5:179155362..179157938,2	K562	blood:
7	chr5:179123586..179129079-chr5:179129217..179136579,19	MCF-7	breast:
8	chr5:179100838..179108153-chr5:179124449..179130181,22	K562	blood:
9	chr5:179129372..179132984-chr5:179141701..179145363,3	K562	blood:
10	chr5:179045239..179052804-chr5:179123707..179130726,40	K562	blood:

No data

Variant related genes	Relation type
CANX	TF binding region
ENSG00000161013	Chromatin interaction
ENSG00000204659	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11738269	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11738720	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739042	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11740569	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741570	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11743232	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11744616	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11746924	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747496	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522263	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469020	0.83[ASN][1000 genomes]
rs1469021	0.83[ASN][1000 genomes]
rs17617068	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17617710	0.86[ASN][1000 genomes]
rs3756614	0.80[ASN][1000 genomes]
rs3797762	0.86[ASN][1000 genomes]
rs3797776	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41458244	0.83[ASN][1000 genomes]
rs4700838	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700840	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701196	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55654737	0.83[ASN][1000 genomes]
rs55827522	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55975622	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56309143	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56335144	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58386410	0.86[ASN][1000 genomes]
rs62404347	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406176	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406177	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406178	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406181	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62406187	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406219	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406223	0.81[ASN][1000 genomes]
rs6601072	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6639	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66902084	0.80[EUR][1000 genomes]
rs6860716	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.86[ASN][1000 genomes]
rs6893300	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6895902	0.86[ASN][1000 genomes]
rs730012	0.83[ASN][1000 genomes]
rs7444006	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7447159	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7704520	0.86[ASN][1000 genomes]
rs7705530	0.86[ASN][1000 genomes]
rs7709723	0.93[ASN][1000 genomes]
rs7715356	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734102	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735702	0.91[AMR][1000 genomes];0.98[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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 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	chr5:179127200-179132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179127400-179137800	Weak transcription	Aorta	Aorta
3	chr5:179127600-179130000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr5:179127600-179132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:179127800-179130200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:179127800-179130200	Weak transcription	Fetal Lung	lung
7	chr5:179127800-179130400	Enhancers	Left Ventricle	heart
8	chr5:179127800-179130400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:179127800-179130600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:179127800-179130600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:179127800-179130600	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:179127800-179130600	Weak transcription	Thymus	Thymus
13	chr5:179127800-179130600	Strong transcription	NHLF	lung
14	chr5:179127800-179130800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:179127800-179130800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:179127800-179130800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr5:179127800-179130800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr5:179127800-179131000	Genic enhancers	Duodenum Mucosa	Duodenum
19	chr5:179127800-179131800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:179127800-179132000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:179127800-179132200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:179127800-179132200	Weak transcription	NH-A	brain
23	chr5:179127800-179132600	Weak transcription	Primary T cells from cord blood	blood
24	chr5:179127800-179133200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:179127800-179133200	Weak transcription	Brain Anterior Caudate	brain
26	chr5:179127800-179133200	Weak transcription	Fetal Brain Female	brain
27	chr5:179127800-179133400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:179127800-179133600	Weak transcription	Brain Angular Gyrus	brain
29	chr5:179127800-179133600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:179127800-179133600	Weak transcription	Brain Substantia Nigra	brain
31	chr5:179127800-179133600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:179127800-179133800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:179127800-179133800	Weak transcription	Colonic Mucosa	Colon
34	chr5:179127800-179134000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:179127800-179134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:179127800-179136000	Weak transcription	HSMMtube	muscle
37	chr5:179127800-179152000	Strong transcription	NHEK	skin
38	chr5:179127800-179156400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:179127800-179156600	Strong transcription	Fetal Stomach	stomach
40	chr5:179127800-179158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:179128000-179130600	Weak transcription	NHDF-Ad	bronchial
42	chr5:179128000-179131000	Genic enhancers	Dnd41	blood
43	chr5:179128000-179132400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:179128000-179135000	Weak transcription	Esophagus	oesophagus
45	chr5:179128200-179130400	Strong transcription	Osteobl	bone
46	chr5:179128200-179131800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:179128200-179156400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:179128400-179130400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:179128400-179130400	Enhancers	Psoas Muscle	Psoas
50	chr5:179128400-179130600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links