Variant report

Variant	rs1322935
Chromosome Location	chr1:78963305-78963306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10489787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058120	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082394	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094298	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725125	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740498	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748050	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs1322933	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322934	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1575397	0.94[LWK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes]
rs28832602	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33994937	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34012602	0.92[ASN][1000 genomes]
rs34077564	1.00[ASN][1000 genomes]
rs34490913	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34528585	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34572897	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34852041	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123627	1.00[ASN][1000 genomes]
rs35324676	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35978825	1.00[ASN][1000 genomes]
rs3766346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766348	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650581	1.00[JPT][hapmap]
rs538976	1.00[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs58710307	0.91[AFR][1000 genomes]
rs59141469	0.92[AFR][1000 genomes]
rs61769118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769130	0.92[AFR][1000 genomes]
rs6690555	0.92[AFR][1000 genomes]
rs6700362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672561	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67351117	0.97[ASN][1000 genomes]
rs688775	0.80[AFR][1000 genomes]
rs72673924	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72673925	0.81[EUR][1000 genomes];1.00[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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv870807	chr1:78867347-79032598	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv871260	chr1:78957859-78976570	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1322935	ST6GALNAC5	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78957800-78966000	Weak transcription	Ovary	ovary
2	chr1:78957800-78966000	Weak transcription	Pancreas	Pancrea
3	chr1:78958000-78965600	Weak transcription	NHLF	lung
4	chr1:78958800-78966200	Weak transcription	Gastric	stomach
5	chr1:78960400-78963400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:78961400-78965200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:78961800-78963600	Active TSS	NHDF-Ad	bronchial
8	chr1:78962400-78963400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:78962400-78964800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:78962400-78965200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:78962400-78973800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:78962600-78963800	Bivalent Enhancer	HUVEC	blood vessel
13	chr1:78962800-78963400	Enhancers	Osteobl	bone
14	chr1:78963000-78963600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:78963200-78963400	Enhancers	Rectal Smooth Muscle	rectum
16	chr1:78963200-78964000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:78963200-78964000	Strong transcription	Muscle Satellite Cultured Cells	--

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