Variant report

Variant	rs11888670
Chromosome Location	chr2:31320834-31320835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10175305	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10188244	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs10189705	0.83[EUR][1000 genomes]
rs10205657	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10490518	0.82[CEU][hapmap]
rs10490519	0.80[MEX][hapmap]
rs1075688	0.88[EUR][1000 genomes]
rs1075689	0.84[EUR][1000 genomes]
rs11124238	0.82[CEU][hapmap]
rs11124239	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11686425	0.87[EUR][1000 genomes]
rs11692265	0.86[EUR][1000 genomes]
rs12712310	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712311	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]
rs12996218	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs13003016	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029054	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1862975	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs1862977	0.89[EUR][1000 genomes]
rs1862978	0.81[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1862979	0.86[EUR][1000 genomes]
rs1862981	0.81[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs1991103	0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs1991104	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2098787	0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs2161832	0.85[EUR][1000 genomes]
rs2161833	0.85[EUR][1000 genomes]
rs2194464	0.80[MEX][hapmap]
rs2194467	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2194468	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2194469	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2365192	0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2365195	0.80[MEX][hapmap]
rs2365196	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365197	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2365199	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2365200	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2365201	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2365205	0.83[EUR][1000 genomes]
rs2365206	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs35285211	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3919588	0.82[CEU][hapmap]
rs4951965	0.83[EUR][1000 genomes]
rs6543598	0.83[EUR][1000 genomes]
rs6543599	0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs6543600	0.89[EUR][1000 genomes]
rs6709814	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6713789	0.85[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6718085	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718097	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722828	0.83[EUR][1000 genomes]
rs6729079	0.82[CHB][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs6732067	0.81[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs6743541	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753457	0.81[EUR][1000 genomes]
rs6760532	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6760971	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7565689	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7570822	0.81[EUR][1000 genomes]
rs7583033	0.82[CHB][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs7583218	0.85[EUR][1000 genomes]
rs7586148	0.81[TSI][hapmap]
rs7600547	0.87[CHB][hapmap];0.85[EUR][1000 genomes]
rs9973425	0.84[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
rs11888670	GALNT14	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31302000-31321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:31302600-31325200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:31307400-31331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:31310600-31346800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:31313000-31321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:31320400-31321600	Enhancers	NHEK	skin
7	chr2:31320600-31321400	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr2:31320600-31337800	Weak transcription	Primary B cells from cord blood	blood
9	chr2:31320800-31321000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:31320800-31321000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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