Variant report

Variant	rs13020788
Chromosome Location	chr2:178480714-178480715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178479419..178481320-chr2:178491408..178493665,2	K562	blood:
2	chr2:178406620..178408509-chr2:178480094..178481704,2	K562	blood:
3	chr2:178479040..178481545-chr2:178589525..178591056,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10170667	0.83[CEU][hapmap]
rs1047884	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497501	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs11678875	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12467363	0.80[ASN][1000 genomes]
rs12471621	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12611503	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12612481	0.95[JPT][hapmap]
rs12612857	0.89[CEU][hapmap]
rs12616259	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs12618542	0.86[YRI][hapmap]
rs12619074	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12624192	0.89[ASN][1000 genomes]
rs12990917	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997716	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13000048	0.80[CEU][hapmap]
rs13008833	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13008857	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs13009207	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13027895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13031008	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034781	0.95[JPT][hapmap]
rs13034886	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs1348849	0.80[CEU][hapmap]
rs1348850	0.89[CEU][hapmap]
rs1358328	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs1405713	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs1405714	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs1405717	0.80[ASN][1000 genomes]
rs1405718	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1453370	0.80[CEU][hapmap]
rs1527401	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530034	0.86[JPT][hapmap]
rs1544002	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1548067	0.89[CEU][hapmap]
rs2166558	0.80[CEU][hapmap]
rs2222711	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2364854	0.84[CEU][hapmap]
rs2365619	0.86[YRI][hapmap]
rs3770005	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3770007	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3770008	0.95[JPT][hapmap]
rs3770009	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3770011	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs3770012	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs3902850	0.80[CEU][hapmap]
rs4144276	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4243388	0.80[CEU][hapmap]
rs4337505	0.95[JPT][hapmap]
rs4470372	0.82[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap]
rs4528793	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs4893822	0.80[CEU][hapmap]
rs4893838	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4893959	0.80[CEU][hapmap]
rs4893962	0.90[CEU][hapmap]
rs4893965	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs4893968	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4893969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893971	0.86[AFR][1000 genomes]
rs4893972	0.95[YRI][hapmap]
rs55792594	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6705405	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs6734426	0.86[YRI][hapmap]
rs6734528	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]
rs6734683	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs6736390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742951	0.80[CEU][hapmap]
rs7587604	0.80[CEU][hapmap]
rs7605609	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7605757	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7606235	0.80[CEU][hapmap]
rs880897	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs880898	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs880899	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs8941	0.80[CEU][hapmap]
rs952746	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	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
9	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
10	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13020788	TTC30A	cis	Lymphoblastoid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
3	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:178468400-178482800	Weak transcription	Fetal Brain Male	brain
6	chr2:178471800-178482600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:178472600-178481000	Weak transcription	Fetal Kidney	kidney
8	chr2:178476000-178481000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:178476400-178482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:178476800-178482600	Weak transcription	HepG2	liver
11	chr2:178477400-178482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:178477600-178482600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:178477800-178482400	Weak transcription	Brain Substantia Nigra	brain
14	chr2:178477800-178482800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:178477800-178482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:178479600-178482600	Weak transcription	HSMM	muscle
17	chr2:178479800-178480800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:178479800-178481000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:178480000-178481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:178480000-178482600	Weak transcription	K562	blood
21	chr2:178480000-178482800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:178480600-178481000	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links