Variant report

Variant	rs531490
Chromosome Location	chr11:66324360-66324361
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66323180..66325641-chr11:66328411..66330736,2	MCF-7	breast:
2	chr11:66311873..66314750-chr11:66320969..66327300,6	K562	blood:

Variant related genes	Relation type
ENSG00000174165	Chromatin interaction
ENSG00000248746	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10791882	0.84[ASN][1000 genomes]
rs1127894	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1671064	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1815739	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2000939	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3018318	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs486584	0.82[ASN][1000 genomes]
rs509556	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs540874	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs545009	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs560556	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs572846	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs615205	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs618838	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs630021	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs677488	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs531490	ACTN3	cis	Muscle Skeletal	GTEx
rs531490	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs531490	CCS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66314400-66327000	Weak transcription	Right Atrium	heart
2	chr11:66314800-66326600	Weak transcription	Psoas Muscle	Psoas
3	chr11:66316400-66325200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:66316800-66325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:66317000-66324800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:66321400-66330400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:66321600-66324600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:66321800-66326400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:66321800-66326400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:66321800-66326400	Weak transcription	Gastric	stomach
13	chr11:66322200-66325800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr11:66323000-66324600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:66323000-66325400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:66323600-66326400	Weak transcription	Pancreas	Pancrea
18	chr11:66323800-66324800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:66323800-66325000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:66323800-66325000	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links