Variant report

Variant	rs1358328
Chromosome Location	chr2:178517532-178517533
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	chr2:178507100..178511896-chr2:178515301..178517578,4	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10167783	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1047884	0.94[JPT][hapmap]
rs11674779	0.80[EUR][1000 genomes]
rs11678875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11682717	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11682753	0.83[ASN][1000 genomes]
rs11890088	0.90[ASN][1000 genomes]
rs12467363	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12469884	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12471621	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475108	0.94[ASN][1000 genomes]
rs12611503	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612481	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12616259	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12990878	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12994392	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12997716	0.89[ASN][1000 genomes]
rs13008833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13008857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13009207	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13020788	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs13034781	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1405714	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1405717	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1405718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1527401	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1527406	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1527407	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530034	0.85[JPT][hapmap]
rs1544002	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2222711	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770005	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770007	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3770008	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3770009	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770010	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770011	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770012	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821006	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4144275	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4144276	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337505	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4470372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4893838	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893969	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs55792594	0.90[ASN][1000 genomes]
rs6433684	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6734528	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]
rs6736390	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7578325	0.89[ASN][1000 genomes]
rs7594362	0.82[ASN][1000 genomes]
rs7605493	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7605609	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7605757	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs880897	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880898	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs880899	0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1358328	TTC30A	cis	Lymphoblastoid	GTEx
rs1358328	TTC30B	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178515200-178519000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:178516000-178518600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr2:178516000-178518600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:178516000-178518800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:178516200-178517800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:178516200-178517800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:178516200-178518400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr2:178516200-178518600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:178516200-178518600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:178516400-178517600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:178516400-178518600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr2:178516600-178517800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:178516600-178518200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr2:178517000-178524400	Weak transcription	Fetal Kidney	kidney
15	chr2:178517200-178518400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:178517200-178518600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr2:178517200-178530800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:178517400-178518600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:178517400-178524200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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