Variant report

Variant	rs12997716
Chromosome Location	chr2:178494629-178494630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178493836..178495394-chr2:178504667..178506617,2	MCF-7	breast:
2	chr2:178494059..178496707-chr2:178497248..178499887,2	K562	blood:
3	chr2:178489030..178493776-chr2:178494411..178499893,10	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10167783	0.89[ASN][1000 genomes]
rs1047884	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11678875	0.92[ASN][1000 genomes]
rs11682717	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11682753	0.82[ASN][1000 genomes]
rs11890088	0.89[ASN][1000 genomes]
rs12467363	0.93[ASN][1000 genomes]
rs12469884	0.89[ASN][1000 genomes]
rs12471621	0.93[ASN][1000 genomes]
rs12475108	0.83[ASN][1000 genomes]
rs12611503	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616259	0.92[ASN][1000 genomes]
rs12619074	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12624192	0.80[ASN][1000 genomes]
rs12990878	0.84[ASN][1000 genomes]
rs12990917	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12994392	0.86[ASN][1000 genomes]
rs13008833	0.92[ASN][1000 genomes]
rs13008857	0.92[ASN][1000 genomes]
rs13009207	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13020788	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13027895	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13031008	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13034781	0.85[ASN][1000 genomes]
rs13034886	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1358328	0.89[ASN][1000 genomes]
rs1405714	0.84[ASN][1000 genomes]
rs1405717	0.93[ASN][1000 genomes]
rs1405718	0.93[ASN][1000 genomes]
rs1527401	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1527406	0.81[ASN][1000 genomes]
rs1527407	0.81[ASN][1000 genomes]
rs1544002	0.81[ASN][1000 genomes]
rs2222711	0.84[ASN][1000 genomes]
rs3770005	0.88[ASN][1000 genomes]
rs3770009	0.84[ASN][1000 genomes]
rs3770010	0.86[ASN][1000 genomes]
rs3770011	0.84[ASN][1000 genomes]
rs3770012	0.84[ASN][1000 genomes]
rs3821006	0.86[ASN][1000 genomes]
rs4144275	0.85[ASN][1000 genomes]
rs4144276	0.89[ASN][1000 genomes]
rs4337505	0.81[ASN][1000 genomes]
rs4470372	0.92[ASN][1000 genomes]
rs4893838	0.84[ASN][1000 genomes]
rs4893968	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4893969	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4893971	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs55792594	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433684	0.81[ASN][1000 genomes]
rs6705405	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6734528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734683	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6736390	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7605493	0.84[ASN][1000 genomes]
rs7605609	0.82[ASN][1000 genomes]
rs880897	0.84[ASN][1000 genomes]
rs880898	0.86[ASN][1000 genomes]
rs880899	0.82[ASN][1000 genomes]

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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv525762	chr2:178494520-178497366	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178484000-178499200	Weak transcription	Pancreas	Pancrea
2	chr2:178488000-178498800	Weak transcription	Fetal Kidney	kidney
3	chr2:178491400-178496400	Weak transcription	K562	blood
4	chr2:178491400-178498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:178491400-178498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:178493200-178498800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:178493800-178494800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:178494000-178495200	Enhancers	Dnd41	blood
9	chr2:178494200-178495400	Enhancers	Fetal Brain Male	brain
10	chr2:178494200-178497800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:178494200-178498000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:178494200-178498200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:178494200-178499200	Weak transcription	Left Ventricle	heart
14	chr2:178494400-178494800	Enhancers	Brain Substantia Nigra	brain
15	chr2:178494400-178495000	Enhancers	Fetal Brain Female	brain
16	chr2:178494400-178495000	Enhancers	GM12878-XiMat	blood
17	chr2:178494400-178497400	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:178494400-178497600	Weak transcription	Brain Germinal Matrix	brain
19	chr2:178494400-178498000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:178494400-178498400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:178494600-178496000	Enhancers	HepG2	liver

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