Variant report

Variant	rs6868242
Chromosome Location	chr5:177942798-177942799
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	chr5:177940111..177942825-chr5:177947320..177948869,2	MCF-7	breast:
2	chr5:177938102..177940198-chr5:177941546..177944250,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1106072	0.89[ASW][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs12514295	0.83[AMR][1000 genomes]
rs12518108	0.83[AMR][1000 genomes]
rs12523125	0.83[AMR][1000 genomes]
rs12651848	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13165074	0.82[MEX][hapmap]
rs1709746	0.85[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs17589948	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs1996222	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1996223	0.81[GIH][hapmap];0.91[MEX][hapmap]
rs2036223	0.81[EUR][1000 genomes]
rs262045	1.00[YRI][hapmap]
rs2647705	0.83[AMR][1000 genomes]
rs34145491	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34653108	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35218983	0.84[AMR][1000 genomes]
rs4976785	0.83[AMR][1000 genomes]
rs539707	0.82[MEX][hapmap]
rs574240	0.82[ASN][1000 genomes]
rs576738	0.81[AMR][1000 genomes]
rs603852	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs67397648	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7379734	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs885306	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv462571	chr5:177898650-177961860	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv600424	chr5:177898650-177961860	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv471059	chr5:177919951-177965696	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6868242	GPRIN1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177933600-177946200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:177936200-177947200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:177942400-177944400	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr5:177942600-177946200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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