Variant report

Variant	rs341061
Chromosome Location	chr11:72382816-72382817
allele	C/T
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	POLR2A	chr11:72382701-72382963	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr11:72382726-72383151	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:72382717-72383090	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:72379745..72382599-chr11:72382781..72384795,2	K562	blood:
2	chr11:72300604..72301466-chr11:72382379..72383160,2	MCF-7	breast:

Variant related genes	Relation type
PDE2A	TF binding region
ENSG00000186642	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10793036	0.80[CHB][hapmap]
rs11235556	0.86[ASN][1000 genomes]
rs11235557	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235558	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146545	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12362256	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363065	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576046	0.88[ASN][1000 genomes]
rs12576058	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12786302	0.86[ASN][1000 genomes]
rs12787293	0.88[ASN][1000 genomes]
rs12797368	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12797791	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs12799451	0.88[ASN][1000 genomes]
rs12802369	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12804316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1391888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs163694	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168175	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872126	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs189332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980089	0.81[CHB][hapmap]
rs2035467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037030	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306609	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs341051	0.83[ASN][1000 genomes]
rs341052	0.93[CHB][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs341053	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs341060	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs341062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34142547	0.88[ASN][1000 genomes]
rs34173798	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs342322	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34285624	0.88[ASN][1000 genomes]
rs34802028	0.88[ASN][1000 genomes]
rs35748558	0.88[ASN][1000 genomes]
rs3758934	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758935	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758936	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781913	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs455611	0.82[ASN][1000 genomes]
rs458275	0.93[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs458575	0.80[CHB][hapmap]
rs56133505	0.83[ASN][1000 genomes]
rs7119321	0.82[ASN][1000 genomes]
rs7126790	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900613	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs900614	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs900615	0.85[EUR][1000 genomes]
rs90409	0.85[CHB][hapmap]
rs907853	0.86[ASN][1000 genomes]
rs907854	0.86[ASN][1000 genomes]
rs907856	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907857	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907858	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs932074	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs932075	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	esv1832864	chr11:72270965-72389125	Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
4	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
5	nsv825991	chr11:72320642-72385221	Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs341061	KRTAP5-10	cis	parietal	SCAN
rs341061	ARAP1	cis	cerebellum	SCAN
rs341061	STARD10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72379000-72384000	Enhancers	Fetal Brain Male	brain
2	chr11:72379200-72384800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr11:72380600-72395400	Weak transcription	Right Atrium	heart
4	chr11:72381000-72383800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:72381000-72385000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:72381200-72383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:72381800-72383200	Bivalent Enhancer	Brain Angular Gyrus	brain
8	chr11:72381800-72384400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:72382000-72383600	Enhancers	Brain Germinal Matrix	brain
10	chr11:72382400-72383000	Enhancers	Fetal Brain Female	brain
11	chr11:72382800-72383400	Active TSS	Brain Anterior Caudate	brain
12	chr11:72382800-72384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links