Variant report

Variant	rs12657817
Chromosome Location	chr5:177879732-177879733
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177768665..177770480-chr5:177878843..177880879,2	K562	blood:
2	chr5:177879706..177881386-chr5:177883345..177884930,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10039491	0.87[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs10051479	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10053433	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10078495	1.00[ASN][1000 genomes]
rs10479493	0.96[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs12516264	0.99[ASN][1000 genomes]
rs12652427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159176	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap]
rs13179262	0.86[ASN][1000 genomes]
rs13179385	0.97[ASN][1000 genomes]
rs1391654	0.96[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs1498617	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1846371	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2133281	0.81[ASN][1000 genomes]
rs2546626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546627	0.95[EUR][1000 genomes]
rs2546628	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2546629	0.96[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2546630	0.92[EUR][1000 genomes]
rs2647688	0.96[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2647693	0.91[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2672819	0.92[EUR][1000 genomes]
rs2672820	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2840140	0.87[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs4288132	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4329031	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs477842	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4976777	0.88[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs55662845	0.96[EUR][1000 genomes]
rs56135911	0.96[EUR][1000 genomes]
rs6601239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67405022	0.99[ASN][1000 genomes]
rs678011	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6867956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725796	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332465	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv1029822	chr5:177872333-177931889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033039	chr5:177873974-177926244	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv537971	chr5:177873974-177926244	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12657817	C2orf3	trans	cerebellum	SCAN
rs12657817	ZNF354B	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177856800-177887200	Weak transcription	Right Atrium	heart
2	chr5:177871800-177880600	Weak transcription	Fetal Thymus	thymus
3	chr5:177874600-177888200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:177877000-177881600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:177877600-177880000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:177877600-177880200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:177877600-177880200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:177877600-177881400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:177877600-177894200	Weak transcription	Spleen	Spleen
10	chr5:177877800-177880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:177877800-177880000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:177877800-177880800	Enhancers	K562	blood
13	chr5:177877800-177895400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:177878000-177888000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:177879200-177881000	Enhancers	Cortex derived primary cultured neurospheres	brain

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