Variant report

Variant	rs1820667
Chromosome Location	chr5:116770989-116770990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:116769502..116772047-chr5:116790908..116792461,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248663	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10035911	0.90[ASN][1000 genomes]
rs10071916	0.90[ASN][1000 genomes]
rs10079714	0.81[ASN][1000 genomes]
rs10477562	0.90[ASN][1000 genomes]
rs10478348	0.90[ASN][1000 genomes]
rs10478349	0.90[ASN][1000 genomes]
rs10478350	0.90[ASN][1000 genomes]
rs13164296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13164536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13165072	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13175962	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13176313	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13176472	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13176885	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13177703	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180710	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180714	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13184765	0.88[EUR][1000 genomes]
rs13354532	0.90[ASN][1000 genomes]
rs13355712	0.81[ASN][1000 genomes]
rs1366184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17141717	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17398971	0.88[EUR][1000 genomes]
rs17839480	0.84[EUR][1000 genomes]
rs2560627	0.90[ASN][1000 genomes]
rs2657043	0.83[ASN][1000 genomes]
rs267059	0.83[ASN][1000 genomes]
rs267060	0.83[ASN][1000 genomes]
rs28454754	0.81[ASN][1000 genomes]
rs34360904	0.84[EUR][1000 genomes]
rs34374339	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183133	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515870	0.84[EUR][1000 genomes]
rs35753719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365600	0.83[ASN][1000 genomes]
rs366335	0.83[ASN][1000 genomes]
rs369130	0.83[ASN][1000 genomes]
rs374057	0.83[ASN][1000 genomes]
rs378387	0.83[ASN][1000 genomes]
rs386139	0.83[ASN][1000 genomes]
rs387069	0.83[ASN][1000 genomes]
rs388253	0.83[ASN][1000 genomes]
rs388643	0.83[ASN][1000 genomes]
rs390818	0.83[ASN][1000 genomes]
rs392437	0.83[ASN][1000 genomes]
rs398793	0.83[ASN][1000 genomes]
rs400845	0.83[ASN][1000 genomes]
rs401607	0.83[ASN][1000 genomes]
rs402131	0.83[ASN][1000 genomes]
rs402578	0.83[ASN][1000 genomes]
rs408218	0.83[ASN][1000 genomes]
rs410212	0.83[ASN][1000 genomes]
rs411705	0.83[ASN][1000 genomes]
rs412087	0.83[ASN][1000 genomes]
rs4133428	0.90[ASN][1000 genomes]
rs428812	0.83[ASN][1000 genomes]
rs435028	0.83[ASN][1000 genomes]
rs445048	0.83[ASN][1000 genomes]
rs55788310	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55912291	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222571	0.81[ASN][1000 genomes]
rs611501	0.83[ASN][1000 genomes]
rs612365	0.83[ASN][1000 genomes]
rs62378254	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62378255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62378256	1.00[EUR][1000 genomes]
rs62378257	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62378258	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62380061	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62380371	0.90[ASN][1000 genomes]
rs62380373	0.90[ASN][1000 genomes]
rs62380374	0.90[ASN][1000 genomes]
rs62380375	0.90[ASN][1000 genomes]
rs62380378	0.90[ASN][1000 genomes]
rs62380379	0.90[ASN][1000 genomes]
rs62380380	0.90[ASN][1000 genomes]
rs62380381	0.90[ASN][1000 genomes]
rs62380382	0.90[ASN][1000 genomes]
rs62380383	0.90[ASN][1000 genomes]
rs62380384	0.90[ASN][1000 genomes]
rs62380385	0.90[ASN][1000 genomes]
rs62380386	0.90[ASN][1000 genomes]
rs66497971	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67546109	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861435	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887390	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899129	0.83[ASN][1000 genomes]
rs72812601	0.90[ASN][1000 genomes]
rs72814413	0.90[ASN][1000 genomes]
rs72814414	0.90[ASN][1000 genomes]
rs962006	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962007	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830457	chr5:116724777-116875060	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv599487	chr5:116732456-116772093	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116769000-116772200	Enhancers	Colon Smooth Muscle	Colon
2	chr5:116769400-116771000	Enhancers	HSMMtube	muscle
3	chr5:116769400-116772400	Enhancers	Rectal Smooth Muscle	rectum
4	chr5:116770000-116771000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:116770200-116773000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:116770400-116772800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:116770400-116773600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:116770600-116772200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:116770600-116772800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:116770600-116774600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:116770800-116771000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:116770800-116772800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:116770800-116772800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:116770800-116773000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:116770800-116773200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links