Variant report

Variant	rs329478
Chromosome Location	chr2:64257746-64257747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64256185..64258127-chr2:64260254..64262848,2	K562	blood:
2	chr2:64251335..64255008-chr2:64255786..64259305,3	MCF-7	breast:
3	chr2:64256991..64258692-chr2:64262523..64264445,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10183479	0.81[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10865344	0.91[YRI][hapmap]
rs11558741	0.88[ASN][1000 genomes]
rs11674020	0.90[ASN][1000 genomes]
rs11676710	1.00[ASN][1000 genomes]
rs11683408	0.96[ASN][1000 genomes]
rs11691987	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs12713498	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12996866	0.88[ASN][1000 genomes]
rs13018690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13431781	0.88[ASN][1000 genomes]
rs1440002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17562177	0.90[ASN][1000 genomes]
rs17562423	0.98[ASN][1000 genomes]
rs193031	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2302808	0.90[ASN][1000 genomes]
rs2439183	0.96[ASN][1000 genomes]
rs2969395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329488	0.91[ASN][1000 genomes]
rs329502	0.85[CHB][hapmap]
rs34122334	0.92[ASN][1000 genomes]
rs34765999	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34777730	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002211	0.90[ASN][1000 genomes]
rs35336851	0.94[ASN][1000 genomes]
rs35480874	1.00[ASN][1000 genomes]
rs35697586	1.00[ASN][1000 genomes]
rs35960986	0.89[ASN][1000 genomes]
rs36033991	0.90[ASN][1000 genomes]
rs36123537	0.98[ASN][1000 genomes]
rs4233930	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4538187	0.81[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.91[YRI][hapmap];0.88[ASN][1000 genomes]
rs4671071	0.83[ASN][1000 genomes]
rs4671073	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs56904032	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6546029	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6546030	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6546032	0.80[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6546033	0.87[ASN][1000 genomes]
rs6546035	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs66980330	0.88[ASN][1000 genomes]
rs6710763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs67308158	0.88[ASN][1000 genomes]
rs6731508	0.88[ASN][1000 genomes]
rs6732746	0.81[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs6755646	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs67615384	0.92[ASN][1000 genomes]
rs67765474	0.90[ASN][1000 genomes]
rs68117986	0.96[ASN][1000 genomes]
rs72808243	0.88[ASN][1000 genomes]
rs72893103	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74181291	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7590399	0.81[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.88[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	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs329478	UGP2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64247600-64262800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:64251200-64273200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:64254000-64258000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:64256800-64262200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:64257200-64262400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:64257400-64257800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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