Variant report

Variant	rs6807784
Chromosome Location	chr3:155136039-155136040
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155135726..155137467-chr3:155146155..155148179,2	MCF-7	breast:
2	chr3:155125953..155128553-chr3:155134009..155136555,2	MCF-7	breast:
3	chr3:155134212..155136487-chr3:155137053..155139235,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11706749	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709568	0.86[CHD][hapmap]
rs11713552	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715278	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11928089	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12487150	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493778	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496803	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12631218	0.90[CHD][hapmap]
rs12696031	0.91[ASW][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13066178	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13081656	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083852	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs13100169	0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs2351	0.88[CHD][hapmap]
rs2352	0.88[CHD][hapmap]
rs35424673	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345113	0.85[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4524323	0.81[ASN][1000 genomes]
rs4630984	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs4679744	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4679745	0.91[CHD][hapmap]
rs4680171	0.86[EUR][1000 genomes]
rs4680172	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs4680173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680174	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680175	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680176	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680177	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680178	0.82[ASN][1000 genomes]
rs4680185	0.88[CHD][hapmap]
rs6440985	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440993	0.86[CHD][hapmap]
rs6440994	0.83[CHD][hapmap]
rs6440995	0.83[CHD][hapmap]
rs6762452	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6794214	0.85[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs6802079	0.91[CHD][hapmap]
rs6807961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612603	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7615026	0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7618495	0.86[CHD][hapmap]
rs7619730	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627097	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823946	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs9829532	0.86[CHD][hapmap]
rs9841365	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848852	0.88[CHD][hapmap]
rs9869956	0.93[CHD][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	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv877679	chr3:155128968-155204939	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6807784	SLC33A1	cis	cerebellum	SCAN
rs6807784	GFM1	cis	cerebellum	SCAN
rs6807784	PLCH1	cis	parietal	SCAN
rs6807784	KCNAB1	cis	cerebellum	SCAN
rs6807784	KCNAB1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155131000-155138800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:155133600-155136400	Enhancers	HMEC	breast
3	chr3:155134000-155136400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:155135000-155136600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:155135000-155138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:155135200-155136200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:155135200-155138000	Weak transcription	Osteobl	bone
8	chr3:155135400-155136800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:155135400-155137000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:155135400-155138800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:155135600-155136400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:155135600-155137600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:155135800-155136600	Enhancers	Brain Anterior Caudate	brain
14	chr3:155135800-155136600	Enhancers	Fetal Stomach	stomach
15	chr3:155135800-155136800	Enhancers	Brain Germinal Matrix	brain
16	chr3:155136000-155136600	Enhancers	Fetal Brain Male	brain
17	chr3:155136000-155136600	Enhancers	Fetal Brain Female	brain
18	chr3:155136000-155136800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:155136000-155141400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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