Variant report

Variant	rs12712311
Chromosome Location	chr2:31315555-31315556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10166079	0.88[EUR][1000 genomes]
rs10175305	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10188244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10189705	0.89[EUR][1000 genomes]
rs10196495	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10205657	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075688	0.89[EUR][1000 genomes]
rs1075689	0.85[EUR][1000 genomes]
rs11124239	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11124240	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11674713	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11686425	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs11692265	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs11888670	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712310	0.92[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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996218	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13003016	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13029054	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862975	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862977	0.90[EUR][1000 genomes]
rs1862978	0.82[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1862979	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs1862981	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1991103	0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1991104	0.92[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs2098787	0.85[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2161832	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2161833	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2194467	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2194468	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2194469	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2365192	0.89[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2365196	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2365197	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365199	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365200	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365201	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2365205	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2365206	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35285211	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4951965	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs6543598	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs6543599	0.89[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs6543600	0.90[EUR][1000 genomes]
rs6709814	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6713789	1.00[CEU][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs6718085	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6718097	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6722828	0.84[EUR][1000 genomes]
rs6729079	0.89[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6732067	0.82[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs6743541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6753457	0.88[EUR][1000 genomes]
rs6760532	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6760971	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7565689	0.89[CEU][hapmap];0.86[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs7570822	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7583033	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7583218	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7586148	0.82[JPT][hapmap]
rs7600547	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9973425	0.85[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12712311	GALNT14	cis	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31297400-31316400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:31302000-31321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:31302600-31325200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:31307400-31331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:31310600-31320800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:31310600-31346800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:31313000-31321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:31313400-31317000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:31314800-31317600	Weak transcription	NHEK	skin
10	chr2:31314800-31320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:31315400-31315600	Weak transcription	HMEC	breast

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