Variant report

Variant	rs6734528
Chromosome Location	chr2:178493731-178493732
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	chr2:178490562..178493751-chr2:178498705..178503907,5	K562	blood:
2	chr2:178489030..178493776-chr2:178494411..178499893,10	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10167783	0.85[ASN][1000 genomes]
rs10170667	0.81[CEU][hapmap]
rs1047884	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497501	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs11678875	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11682717	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11890088	0.85[ASN][1000 genomes]
rs12467363	0.90[ASN][1000 genomes]
rs12469884	0.86[ASN][1000 genomes]
rs12471621	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12611503	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612481	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs12612857	0.89[CEU][hapmap]
rs12616259	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12618542	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs12619074	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12990878	0.81[ASN][1000 genomes]
rs12990917	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12994392	0.83[ASN][1000 genomes]
rs12997716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13008833	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13008857	0.84[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs13009207	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13020788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13027895	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13031008	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13034781	0.80[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13034886	1.00[ASW][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1348850	0.89[CEU][hapmap]
rs1358328	0.84[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs1405713	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs1405714	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs1405717	0.90[ASN][1000 genomes]
rs1405718	0.84[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs1527401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530034	0.85[JPT][hapmap]
rs1544002	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs1548067	0.89[CEU][hapmap]
rs2222711	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2364854	0.82[CEU][hapmap]
rs2365619	0.93[ASW][hapmap];0.86[YRI][hapmap]
rs3770005	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs3770007	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3770008	1.00[JPT][hapmap]
rs3770009	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770010	0.83[ASN][1000 genomes]
rs3770011	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs3770012	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs3821006	0.83[ASN][1000 genomes]
rs4144275	0.81[ASN][1000 genomes]
rs4144276	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4337505	1.00[JPT][hapmap]
rs4470372	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4528793	0.89[CEU][hapmap];0.84[YRI][hapmap]
rs4893838	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4893962	0.89[CEU][hapmap]
rs4893965	0.81[ASW][hapmap];0.89[CEU][hapmap];0.85[YRI][hapmap]
rs4893968	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4893969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4893971	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4893972	1.00[ASW][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap]
rs55792594	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6705405	1.00[ASW][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6734426	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs6734683	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6736390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605493	0.81[ASN][1000 genomes]
rs7605609	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs7605757	0.80[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs880897	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs880898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs880899	1.00[CHB][hapmap];0.84[JPT][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	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	nsv819130	chr2:178493720-178494177	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6734528	TTC30B	cis	parietal	SCAN
rs6734528	TTC30A	cis	Lymphoblastoid	GTEx

Chromatin state (count:20 , 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	chr2:178491000-178493800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:178491000-178494600	Weak transcription	HepG2	liver
5	chr2:178491200-178493800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:178491200-178493800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:178491400-178493800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:178491400-178493800	Weak transcription	Brain Germinal Matrix	brain
9	chr2:178491400-178494400	Weak transcription	Fetal Brain Female	brain
10	chr2:178491400-178496400	Weak transcription	K562	blood
11	chr2:178491400-178498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:178491400-178498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:178491600-178493800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:178491800-178494200	Weak transcription	Fetal Brain Male	brain
15	chr2:178493200-178494000	Enhancers	Brain Substantia Nigra	brain
16	chr2:178493200-178498800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:178493400-178494200	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:178493400-178494400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:178493600-178494000	Enhancers	GM12878-XiMat	blood
20	chr2:178493600-178494200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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