Variant report

Variant	rs645621
Chromosome Location	chr11:65490756-65490757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:65490737-65490787	HRE	kidney:	n/a
2	chr11:65490737-65490787	HUVEC	blood vessel:	n/a
3	chr11:65490737-65490787	NT2-D1	testis:	n/a
4	chr11:65490737-65490787	LNCaP	prostate:	n/a
5	chr11:65490737-65490787	HepG2	liver:	n/a
6	chr11:65490737-65490787	GM19239	blood:	n/a
7	chr11:65490737-65490787	CMK	blood:	n/a
8	chr11:65490737-65490787	NB4	blood:	n/a
9	chr11:65490737-65490787	NHBE	bronchial:	n/a
10	chr11:65490737-65490787	BJ	skin:	n/a
11	chr11:65490737-65490787	HPAEpiC	pulmonary alveolar:	n/a
12	chr11:65490737-65490787	SK-N-MC	brain:	n/a
13	chr11:65490737-65490787	AG09319	gingival:	n/a
14	chr11:65490737-65490787	A549	lung:	n/a
15	chr11:65490737-65490787	PFSK-1	brain:	n/a
16	chr11:65490737-65490787	SK-N-SH_RA	brain:	n/a
17	chr11:65490737-65490787	HIPEpiC	eye:	n/a
18	chr11:65490737-65490787	AG04450	lung:	fetal
19	chr11:65490737-65490787	GM12878	blood:	n/a
20	chr11:65490737-65490787	ovcar-3	ovarian:	n/a
21	chr11:65490737-65490787	Caco-2	colon:	n/a
22	chr11:65490737-65490787	HMEC	breast:	n/a
23	chr11:65490737-65490787	HRCEpiC	kidney:	n/a
24	chr11:65490737-65490787	Jurkat	blood:	n/a
25	chr11:65490737-65490787	K562	blood:	n/a
26	chr11:65490737-65490787	GM12891	blood:	n/a
27	chr11:65490737-65490787	PANC-1	pancreas:	n/a
28	chr11:65490737-65490787	T-47D	breast:	n/a
29	chr11:65490737-65490787	IMR90	lung:	fetal
30	chr11:65490737-65490787	SK-N-SH	brain:	n/a
31	chr11:65490737-65490787	PrEC	prostate:	n/a
32	chr11:65490737-65490787	HL-60	blood:	n/a
33	chr11:65490737-65490787	GM06990	blood:	n/a
34	chr11:65490737-65490787	H1-hESC	embryonic stem cell:	embryo
35	chr11:65490737-65490787	ProgFib	skin:	n/a
36	chr11:65490737-65490787	MCF10A-Er-Src	breast:	n/a
37	chr11:65490737-65490787	HEEpiC	esophagus:	n/a
38	chr11:65490737-65490787	HCT-116	colon:	n/a
39	chr11:65490737-65490787	BE2_C	brain:	n/a
40	chr11:65490737-65490787	NH-A	brain:	n/a
41	chr11:65490737-65490787	AG04449	skin:	fetal
42	chr11:65490737-65490787	AG10803	skin:	n/a
43	chr11:65490737-65490787	HAEpiC	amniotic membrane:	n/a
44	chr11:65490737-65490787	GM12892	blood:	n/a
45	chr11:65490737-65490787	HNPCEpiC	eye:	n/a
46	chr11:65490737-65490787	HRPEpiC	eye:	n/a
47	chr11:65490737-65490787	RPTEC	kidney:	n/a
48	chr11:65490737-65490787	NHDF-neo	bronchial:	n/a
49	chr11:65490737-65490787	AoSMC	blood vessel:	n/a
50	chr11:65490737-65490787	Hela-S3	cervix:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65489436..65492400-chr11:65547106..65548686,2	MCF-7	breast:
2	chr11:65419136..65421674-chr11:65489039..65492685,3	K562	blood:
3	chr11:65488838..65491538-chr11:65497490..65499869,2	K562	blood:
4	chr11:65488196..65490800-chr11:65684778..65687737,2	MCF-7	breast:
5	chr11:65485735..65490975-chr11:65621882..65626984,8	K562	blood:
6	chr11:65487463..65490934-chr11:65492571..65495479,8	K562	blood:
7	chr11:65487099..65491310-chr11:65543476..65547938,6	MCF-7	breast:

No data

Variant related genes	Relation type
RNASEH2C	CpG island
KRT8P26	CpG island
ENSG00000175827	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000214659	Chromatin interaction
ENSG00000254470	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1108922	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1151500	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1151501	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2509946	0.93[AFR][1000 genomes]
rs2510030	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3953806	0.86[CHB][hapmap]
rs480989	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs487264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488170	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930298	0.90[EUR][1000 genomes]
rs521678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs534414	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552312	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555903	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55796623	0.81[EUR][1000 genomes]
rs563427	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs565267	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs593982	0.91[CEU][hapmap];0.84[GIH][hapmap]
rs603509	0.91[CEU][hapmap]
rs618456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs680948	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72939198	0.84[EUR][1000 genomes];0.91[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	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65488400-65491600	Weak transcription	Right Atrium	heart
2	chr11:65488400-65492400	Weak transcription	Placenta	Placenta
3	chr11:65488400-65494200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:65488400-65496200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:65490600-65494000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links