Variant report

Variant	rs58557417
Chromosome Location	chr3:161086283-161086284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:161024873..161027806-chr3:161085286..161087243,2	MCF-7	breast:
2	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
3	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
4	chr3:160999506..161001764-chr3:161085890..161088412,2	MCF-7	breast:
5	chr3:160787784..160789478-chr3:161085891..161088171,2	MCF-7	breast:
6	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
7	chr3:161086150..161088854-chr6:26156323..26158210,2	MCF-7	breast:
8	chr11:46622262..46624365-chr3:161085688..161088044,2	MCF-7	breast:
9	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
10	chr3:160962510..160966697-chr3:161085167..161089151,3	MCF-7	breast:
11	chr3:63914213..63915723-chr3:161085984..161088284,2	MCF-7	breast:
12	chr3:160790555..160793419-chr3:161085897..161087405,2	MCF-7	breast:
13	chr2:199451456..199452956-chr3:161085880..161088129,3	MCF-7	breast:
14	chr3:160817799..160820067-chr3:161084630..161087125,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000168298	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12632537	0.80[EUR][1000 genomes]
rs12634006	0.88[EUR][1000 genomes]
rs55814004	0.81[ASN][1000 genomes]
rs57278490	0.84[EUR][1000 genomes]
rs57496534	0.84[EUR][1000 genomes]
rs57803909	0.84[EUR][1000 genomes]
rs58350275	0.84[EUR][1000 genomes]
rs58562874	0.84[EUR][1000 genomes]
rs59541314	0.80[EUR][1000 genomes]
rs59761692	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs59964190	0.84[EUR][1000 genomes]
rs60400555	0.80[EUR][1000 genomes]
rs60612225	0.84[EUR][1000 genomes]
rs60684226	0.84[EUR][1000 genomes]
rs61217744	0.88[EUR][1000 genomes]
rs73878307	0.88[EUR][1000 genomes]
rs73878308	0.88[EUR][1000 genomes]
rs73878311	0.88[EUR][1000 genomes]
rs73878313	0.80[EUR][1000 genomes]
rs73878321	0.80[EUR][1000 genomes]
rs73878322	0.80[EUR][1000 genomes]
rs73878324	0.80[EUR][1000 genomes]
rs73878325	0.80[EUR][1000 genomes]
rs73878328	0.80[EUR][1000 genomes]
rs7625217	0.84[EUR][1000 genomes]
rs873183	0.88[EUR][1000 genomes]
rs896080	0.88[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv963570	chr3:161076656-161088849	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161081800-161087200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:161084400-161087400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:161084400-161088400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:161084400-161088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:161084600-161088200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:161085200-161087600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:161085400-161088200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:161085600-161088600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:161085800-161087200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:161085800-161088400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:161086200-161088600	Weak transcription	Stomach Mucosa	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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