Variant report

Variant	rs2299705
Chromosome Location	chr20:52657462-52657463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
2	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
3	chr20:52655188..52657937-chr20:55839006..55840900,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11905945	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381983	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381984	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557853	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072128	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2107327	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2189502	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2214530	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2238701	0.90[ASN][1000 genomes]
rs2276487	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276488	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276489	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276491	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2299698	0.89[EUR][1000 genomes]
rs2299699	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299701	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299702	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299707	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299711	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299712	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299715	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299718	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2870304	0.86[EUR][1000 genomes]
rs34973146	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35883829	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091807	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6091808	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6091811	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6091812	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6097749	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6123344	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6123345	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6127058	0.94[EUR][1000 genomes]
rs6127060	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6127061	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6127062	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6127063	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6127065	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6127066	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6127068	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6127072	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6127073	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67082409	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71323984	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133436	0.94[EUR][1000 genomes]
rs732344	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765348	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:82 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	esv2763673	chr20:52637074-52668126	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv3419	chr20:52637581-52672115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
5	nsv1064465	chr20:52643155-52658639	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv437187	chr20:52644514-52660120	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv1058315	chr20:52644518-52658639	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv1064456	chr20:52644721-52658639	Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv1055799	chr20:52644770-52657717	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1059551	chr20:52644770-52658639	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv1067222	chr20:52644856-52658061	Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv1060500	chr20:52644856-52658639	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv1065821	chr20:52644856-52662562	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
14	nsv912939	chr20:52646029-52660741	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv912940	chr20:52646029-52663409	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
16	esv3513136	chr20:52646045-52659093	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
17	esv3513133	chr20:52646370-52658993	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
18	esv3513132	chr20:52646668-52658237	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
19	esv3454655	chr20:52646917-52658133	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
20	nsv586235	chr20:52646926-52657797	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
21	nsv586236	chr20:52646926-52658001	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
22	nsv517164	chr20:52646926-52660741	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv912941	chr20:52646926-52660741	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
24	nsv912942	chr20:52646926-52663409	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
25	esv3513138	chr20:52646952-52658112	Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
26	esv3513135	chr20:52646964-52658088	Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
27	esv3454654	chr20:52646970-52658079	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
28	esv3513139	chr20:52646987-52658036	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
29	esv3513137	chr20:52646999-52658057	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
30	esv3513134	chr20:52647007-52658053	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
31	esv3454656	chr20:52647065-52658009	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
32	esv3513141	chr20:52647065-52658009	Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
33	esv13873	chr20:52647106-52658080	Weak transcription Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
34	nsv1055315	chr20:52647808-52658061	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
35	nsv1064515	chr20:52647808-52658561	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
36	nsv1059526	chr20:52647808-52658639	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
37	esv2421391	chr20:52647808-52658651	Weak transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
38	nsv442485	chr20:52647808-52658651	Weak transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
39	nsv1059343	chr20:52647808-52662562	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
40	nsv1065004	chr20:52647808-52665631	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
41	esv2760671	chr20:52647808-52665643	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
42	nsv1055891	chr20:52647808-52666885	Enhancers Strong transcription Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
43	nsv1067336	chr20:52647808-52668126	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
44	nsv1065888	chr20:52647808-52670378	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
45	nsv586244	chr20:52647823-52657797	Enhancers Weak transcription	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
46	nsv586245	chr20:52647823-52658001	Weak transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
47	nsv586246	chr20:52647823-52660741	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
48	nsv586247	chr20:52647823-52663409	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
49	nsv433324	chr20:52647823-52663783	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
50	nsv586248	chr20:52647823-52663783	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52655200-52658200	Enhancers	Fetal Stomach	stomach
6	chr20:52657000-52657800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:52657000-52657800	Enhancers	HSMMtube	muscle
8	chr20:52657200-52657600	Enhancers	NHDF-Ad	bronchial
9	chr20:52657400-52658600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links