Variant report

Variant	rs11682772
Chromosome Location	chr2:64550188-64550189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64549162..64550674-chr2:64718526..64720700,2	K562	blood:
2	chr2:64549497..64551574-chr2:64555281..64557791,2	K562	blood:
3	chr2:64364705..64366411-chr2:64549712..64552538,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10182618	0.85[EUR][1000 genomes]
rs10187442	0.86[ASN][1000 genomes]
rs10203643	0.94[CEU][hapmap];0.85[MEX][hapmap]
rs1030407	0.84[ASN][1000 genomes]
rs1030409	0.84[ASN][1000 genomes]
rs1030410	0.85[ASN][1000 genomes]
rs10865345	0.86[EUR][1000 genomes]
rs11125996	0.85[ASN][1000 genomes]
rs11673882	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883600	0.85[ASN][1000 genomes]
rs1974976	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2162380	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2555423	0.84[ASN][1000 genomes]
rs4485554	0.86[ASN][1000 genomes]
rs4597511	0.86[ASN][1000 genomes]
rs4671086	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671561	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671562	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671563	0.94[CEU][hapmap];0.85[MEX][hapmap]
rs6546064	0.86[ASN][1000 genomes]
rs6546065	0.86[ASN][1000 genomes]
rs66506765	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714101	0.83[ASN][1000 genomes]
rs6724171	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6737527	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6740438	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6748843	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6758664	0.85[ASN][1000 genomes]
rs7561343	0.84[ASN][1000 genomes]
rs7565077	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7585084	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs890478	0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs919123	0.83[ASN][1000 genomes]
rs919124	0.83[ASN][1000 genomes]
rs919125	0.84[ASN][1000 genomes]
rs919126	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs919127	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs930020	0.86[ASN][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	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11682772	PELI1	cis	parietal	SCAN
rs11682772	AHSA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64540000-64554200	Weak transcription	Fetal Brain Female	brain
2	chr2:64540200-64554600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:64540800-64554600	Weak transcription	Right Atrium	heart
4	chr2:64546000-64552000	Weak transcription	Thymus	Thymus
5	chr2:64549000-64550200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:64549000-64550800	Enhancers	Fetal Muscle Leg	muscle
7	chr2:64549000-64551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:64549200-64555800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:64549400-64550600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:64549400-64550800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:64549400-64551000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:64549400-64553400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:64549400-64555200	Weak transcription	Placenta	Placenta
14	chr2:64549600-64554400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:64549800-64550200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr2:64549800-64550400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:64549800-64555000	Weak transcription	Fetal Lung	lung
18	chr2:64550000-64550400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:64550000-64550800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:64550000-64550800	Enhancers	Placenta Amnion	Placenta Amnion

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