Variant report

Variant	rs6822396
Chromosome Location	chr4:87393537-87393538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87373116..87375206-chr4:87393123..87394680,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109339	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10008165	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs10023787	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs10029671	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10031843	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1021101	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11097115	0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs11947018	0.84[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11947775	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1481833	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs17011924	0.95[ASN][1000 genomes]
rs17418221	0.91[ASN][1000 genomes]
rs17418531	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17418801	0.95[ASN][1000 genomes]
rs17418878	0.94[ASN][1000 genomes]
rs17419295	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs17452467	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17452556	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28483710	0.82[ASN][1000 genomes]
rs4235081	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4277747	0.85[ASN][1000 genomes]
rs4404513	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4405982	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4407468	0.91[ASN][1000 genomes]
rs4452393	0.90[ASN][1000 genomes]
rs4466012	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4511966	0.90[ASN][1000 genomes]
rs4513526	0.82[ASN][1000 genomes]
rs4529013	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4552430	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4607180	0.91[ASN][1000 genomes]
rs4622964	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4640633	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693147	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4693772	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693776	0.91[ASN][1000 genomes]
rs4693777	0.90[ASN][1000 genomes]
rs55653332	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55654230	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55660529	0.94[ASN][1000 genomes]
rs55722156	0.95[ASN][1000 genomes]
rs55746316	0.82[ASN][1000 genomes]
rs55757426	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55773619	0.82[ASN][1000 genomes]
rs55814693	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55842318	0.91[ASN][1000 genomes]
rs55872468	0.91[ASN][1000 genomes]
rs55879246	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55881335	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55908925	0.91[ASN][1000 genomes]
rs55930543	0.91[ASN][1000 genomes]
rs55969415	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55982489	0.91[ASN][1000 genomes]
rs56009992	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56164000	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56178389	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56222033	0.94[ASN][1000 genomes]
rs56296936	0.82[ASN][1000 genomes]
rs56348925	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56353461	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59644743	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61152200	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6531932	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs67341369	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs67523832	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67928053	0.82[ASN][1000 genomes]
rs6838659	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847139	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72664002	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72665711	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72665712	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72665714	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665719	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665722	0.92[ASN][1000 genomes]
rs72665724	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72665725	0.92[ASN][1000 genomes]
rs72665729	0.91[ASN][1000 genomes]
rs72665734	0.91[ASN][1000 genomes]
rs72665736	0.91[ASN][1000 genomes]
rs72665737	0.91[ASN][1000 genomes]
rs72665738	0.91[ASN][1000 genomes]
rs72665740	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665744	0.91[ASN][1000 genomes]
rs72665746	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72665752	0.91[ASN][1000 genomes]
rs72665753	0.90[ASN][1000 genomes]
rs72665756	0.90[ASN][1000 genomes]
rs72665759	0.83[ASN][1000 genomes]
rs72665762	0.83[ASN][1000 genomes]
rs72665769	0.85[ASN][1000 genomes]
rs72665771	0.82[ASN][1000 genomes]
rs7435744	0.90[ASN][1000 genomes]
rs7673698	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7675845	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7679269	0.88[ASN][1000 genomes]
rs7694723	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7695011	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7697819	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9307020	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs9683663	0.95[ASN][1000 genomes]
rs9993042	0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]

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	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6822396	HPSE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87383600-87393600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:87388400-87393600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:87388400-87393600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:87388600-87393600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:87389200-87393600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:87389400-87393600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:87389600-87393800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:87389800-87393600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:87392800-87395200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr4:87393000-87395600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:87393200-87395000	Enhancers	Dnd41	blood
12	chr4:87393200-87395600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr4:87393400-87394800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:87393400-87396400	Enhancers	HUES64 Cell Line	embryonic stem cell

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