Variant report

Variant	rs2271688
Chromosome Location	chr12:50259529-50259530
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50259278..50261065-chr12:50464788..50467159,2	K562	blood:
2	chr12:50258974..50260618-chr12:50366779..50369622,2	MCF-7	breast:
3	chr12:50259475..50261235-chr12:50302095..50303974,2	MCF-7	breast:
4	chr12:50258046..50259934-chr12:50399287..50401649,2	MCF-7	breast:
5	chr12:50170376..50172143-chr12:50258394..50260601,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044677	0.83[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747567	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747568	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783321	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783323	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783326	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875984	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875986	0.87[EUR][1000 genomes]
rs10875987	0.83[EUR][1000 genomes]
rs11169167	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1563168	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869504	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965873	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1975732	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336059	0.80[EUR][1000 genomes]
rs3741557	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741558	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4290311	0.82[EUR][1000 genomes]
rs4391887	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4898512	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4898513	0.96[EUR][1000 genomes]
rs4898536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4898537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4898539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67723963	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs706797	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs706798	0.87[CEU][hapmap];0.86[TSI][hapmap]
rs7133995	1.00[ASN][1000 genomes]
rs7137210	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295882	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302465	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306374	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307673	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310206	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967564	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969178	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836967	0.87[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs836969	0.84[EUR][1000 genomes]
rs836970	0.82[EUR][1000 genomes]
rs897057	0.87[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs9805137	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv975486	chr12:50247649-50259548	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2271688	C12orf62	cis	parietal	SCAN
rs2271688	BCDIN3D	cis	parietal	SCAN
rs2271688	TMBIM6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50237600-50261200	Weak transcription	Right Atrium	heart
2	chr12:50257800-50259800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr12:50258000-50261200	Weak transcription	Fetal Intestine Large	intestine
4	chr12:50258200-50260000	Enhancers	Fetal Brain Male	brain
5	chr12:50258400-50260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:50258400-50260800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:50258400-50261000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:50258600-50260600	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:50258600-50260600	Weak transcription	HSMM	muscle
10	chr12:50258600-50260800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:50258600-50260800	Weak transcription	Esophagus	oesophagus
12	chr12:50258600-50261000	Weak transcription	Fetal Heart	heart
13	chr12:50258800-50260600	Weak transcription	Fetal Brain Female	brain
14	chr12:50259200-50259600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:50259200-50260600	Weak transcription	HSMMtube	muscle

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