Variant report

Variant	rs55957739
Chromosome Location	chr5:154496135-154496136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr5:154496028-154496883	T-47D	breast:	n/a	n/a
2	HNF4A	chr5:154495977-154496320	HepG2	liver:	n/a	chr5:154496177-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496177-154496192 chr5:154496178-154496191 chr5:154496179-154496191 chr5:154496177-154496192 chr5:154496176-154496194 chr5:154496179-154496191 chr5:154496178-154496186 chr5:154496179-154496191 chr5:154496177-154496192 chr5:154496179-154496191
3	GATA3	chr5:154495927-154497013	T-47D	breast:	n/a	n/a
4	ESR1	chr5:154495969-154496967	T-47D	breast:	n/a	n/a
5	ESR1	chr5:154495963-154496905	T-47D	breast:	n/a	n/a
6	EP300	chr5:154495955-154496979	T-47D	breast:	n/a	n/a
7	FOXA2	chr5:154496039-154496300	HepG2	liver:	n/a	n/a
8	FOXA1	chr5:154495986-154497114	T-47D	breast:	n/a	n/a
9	GATA3	chr5:154496040-154497008	T-47D	breast:	n/a	n/a
10	HNF4G	chr5:154495925-154496378	HepG2	liver:	n/a	chr5:154496177-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496177-154496192 chr5:154496178-154496191 chr5:154496179-154496191 chr5:154496176-154496194 chr5:154496179-154496191 chr5:154496178-154496186 chr5:154496178-154496193 chr5:154496179-154496191 chr5:154496177-154496192 chr5:154496179-154496191
11	EP300	chr5:154496052-154496919	T-47D	breast:	n/a	n/a
12	HNF4A	chr5:154496013-154496261	HepG2	liver:	n/a	chr5:154496177-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496177-154496192 chr5:154496178-154496191 chr5:154496179-154496191 chr5:154496177-154496192 chr5:154496176-154496194 chr5:154496179-154496191 chr5:154496178-154496186 chr5:154496179-154496191 chr5:154496177-154496192 chr5:154496179-154496191
13	ESR1	chr5:154496094-154496851	T-47D	breast:	n/a	n/a
14	HNF4G	chr5:154496022-154496351	HepG2	liver:	n/a	chr5:154496177-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496179-154496192 chr5:154496177-154496192 chr5:154496178-154496191 chr5:154496179-154496191 chr5:154496176-154496194 chr5:154496179-154496191 chr5:154496178-154496186 chr5:154496178-154496193 chr5:154496179-154496191 chr5:154496177-154496192 chr5:154496179-154496191
15	FOXA1	chr5:154496046-154496937	T-47D	breast:	n/a	n/a
16	ESR1	chr5:154495965-154496924	T-47D	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF4B-1	chr5:154496130-154496238	NONHSAT104729
2	lnc-KIF4B-1	chr5:154496110-154496238	NONHSAT104728
3	lnc-KIF4B-1	chr5:154496110-154496238	FPKM1_group_26577_transcript_2

Variant related genes	Relation type
ENSG00000253646	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10035182	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10037186	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10050836	0.89[ASN][1000 genomes]
rs10060354	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10066196	0.89[ASN][1000 genomes]
rs10066219	0.89[ASN][1000 genomes]
rs10066223	0.89[ASN][1000 genomes]
rs10076907	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10476814	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469446	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1549647	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549648	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17572520	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985783	0.89[EUR][1000 genomes]
rs2081965	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081966	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35161960	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35479770	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35656480	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580136	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7702812	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961812	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883059	chr5:154457905-154556230	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv462492	chr5:154489393-154523910	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv600091	chr5:154489393-154523910	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154495400-154496800	Enhancers	HepG2	liver
2	chr5:154495800-154496800	Enhancers	Placenta Amnion	Placenta Amnion

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