Variant report

Variant	rs488498
Chromosome Location	chr5:68484419-68484420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr5:68484372-68486482	SK-N-SH	brain:	n/a	chr5:68485303-68485318 chr5:68485301-68485316
2	POLR2A	chr5:68484215-68484485	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:68484284-68486331	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3AK20	chr5:68484381-68486009	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:68484208..68487030-chr5:68662372..68666589,5	K562	blood:
2	chr5:68472735..68477267-chr5:68482092..68486946,8	MCF-7	breast:
3	chr5:68389777..68391751-chr5:68483907..68486743,2	MCF-7	breast:
4	chr5:68388464..68391397-chr5:68483791..68487195,4	K562	blood:
5	chr5:68388453..68391488-chr5:68483791..68487092,6	K562	blood:
6	chr5:68483901..68487830-chr5:68528757..68532922,9	K562	blood:
7	chr5:68470678..68474023-chr5:68481300..68486180,5	MCF-7	breast:
8	chr5:68461460..68464018-chr5:68483608..68486992,6	MCF-7	breast:
9	chr5:68483355..68487362-chr5:68663859..68666403,7	K562	blood:
10	chr5:68484254..68487485-chr5:68512131..68515372,4	K562	blood:
11	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC125-1	chr5:68483212-68485293	NONHSAT101896

No data

Variant related genes	Relation type
CENPH	TF binding region
ENSG00000134057	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000145740	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10063757	0.91[EUR][1000 genomes]
rs10940209	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10940210	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11748974	0.80[ASN][1000 genomes]
rs13175606	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs151589	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs163444	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164709	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs164715	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164789	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1650779	0.86[ASN][1000 genomes]
rs171212	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184747	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1976103	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2130757	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2171148	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172056	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2242350	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2291519	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291520	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2450230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450246	0.84[ASN][1000 genomes]
rs28602964	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28768211	0.90[EUR][1000 genomes]
rs2930945	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2930949	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2930951	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932767	0.84[ASN][1000 genomes]
rs2932772	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932773	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932774	0.83[EUR][1000 genomes]
rs2932775	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932776	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932782	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972361	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972366	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972377	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2972378	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2972381	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972386	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972387	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972388	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34893396	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs350104	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350106	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs350107	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350109	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350115	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350116	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350122	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350123	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351424	0.87[ASN][1000 genomes]
rs35308484	0.92[EUR][1000 genomes]
rs353656	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs379106	0.87[ASN][1000 genomes]
rs386640	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3934528	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077460	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs419902	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426392	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4266362	0.81[ASN][1000 genomes]
rs4362903	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4421064	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4541612	0.82[ASN][1000 genomes]
rs4629549	0.83[ASN][1000 genomes]
rs603029	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62373164	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6450026	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6450027	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs651076	0.85[ASN][1000 genomes]
rs676012	0.93[EUR][1000 genomes]
rs676879	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6866993	0.83[ASN][1000 genomes]
rs6876783	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs693725	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7733556	0.83[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	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	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
2	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
3	chr5:68471200-68484600	Weak transcription	Primary T cells from cord blood	blood
4	chr5:68471200-68484600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:68471400-68484600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:68471400-68484600	Weak transcription	Liver	Liver
7	chr5:68471400-68484600	Weak transcription	Brain Substantia Nigra	brain
8	chr5:68471400-68484600	Weak transcription	Spleen	Spleen
9	chr5:68471600-68484600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:68471600-68484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:68472000-68484600	Weak transcription	Ovary	ovary
12	chr5:68472200-68484600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:68472400-68484600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:68473400-68484600	Weak transcription	Thymus	Thymus
15	chr5:68473600-68484600	Weak transcription	Primary B cells from cord blood	blood
16	chr5:68473800-68484600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:68474400-68484600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:68474600-68484600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:68482000-68484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:68484200-68484600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:68484200-68484600	Enhancers	Placenta	Placenta
22	chr5:68484200-68484800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:68484200-68485000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:68484200-68485800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:68484200-68485800	Active TSS	Brain Germinal Matrix	brain
26	chr5:68484400-68484600	Active TSS	H1 Cell Line	embryonic stem cell
27	chr5:68484400-68484600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:68484400-68484600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:68484400-68484600	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr5:68484400-68484600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:68484400-68484600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:68484400-68484600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr5:68484400-68484600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr5:68484400-68484600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:68484400-68484600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr5:68484400-68484600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr5:68484400-68484600	Active TSS	Brain Angular Gyrus	brain
38	chr5:68484400-68484600	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr5:68484400-68484600	Active TSS	Colon Smooth Muscle	Colon
40	chr5:68484400-68484600	Active TSS	Duodenum Mucosa	Duodenum
41	chr5:68484400-68484600	Enhancers	Esophagus	oesophagus
42	chr5:68484400-68484600	Enhancers	Fetal Heart	heart
43	chr5:68484400-68484600	Enhancers	Fetal Muscle Trunk	muscle
44	chr5:68484400-68484600	Enhancers	Fetal Thymus	thymus
45	chr5:68484400-68484600	Flanking Active TSS	Pancreas	Pancrea
46	chr5:68484400-68484600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr5:68484400-68484600	Active TSS	Rectal Smooth Muscle	rectum
48	chr5:68484400-68484600	Active TSS	Right Ventricle	heart
49	chr5:68484400-68484600	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr5:68484400-68484600	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links