Variant report

Variant	rs964533
Chromosome Location	chr3:160749019-160749020
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160748979..160751725-chr3:160821249..160823513,2	MCF-7	breast:
2	chr3:160746924..160750622-chr3:160787755..160791172,3	MCF-7	breast:
3	chr3:160739507..160741947-chr3:160747617..160749551,2	MCF-7	breast:
4	chr3:160748601..160749476-chr3:160818403..160819285,3	MCF-7	breast:
5	chr3:160748629..160749475-chr3:161057341..161057842,2	MCF-7	breast:
6	chr3:160748960..160749535-chr3:160759816..160760384,2	MCF-7	breast:
7	chr3:160717602..160719198-chr3:160748866..160750938,2	MCF-7	breast:
8	chr3:160748438..160750159-chr3:160785119..160786787,2	MCF-7	breast:
9	chr3:160747461..160750414-chr3:161128370..161130411,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10433352	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711152	1.00[CEU][hapmap]
rs11713093	0.83[EUR][1000 genomes]
rs11715733	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap]
rs11720263	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11922957	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11922959	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12696112	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12696113	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060718	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13062651	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13071892	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13071999	1.00[CEU][hapmap]
rs13073059	1.00[CEU][hapmap]
rs13085336	0.90[CEU][hapmap]
rs13098896	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13256	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1345156	1.00[CEU][hapmap]
rs1374787	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1374790	0.80[JPT][hapmap]
rs1374795	0.85[JPT][hapmap]
rs1447610	1.00[CEU][hapmap]
rs1447622	1.00[CEU][hapmap]
rs1562464	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1599388	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16831886	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1868105	1.00[CEU][hapmap]
rs1868107	1.00[CEU][hapmap]
rs1868109	0.90[JPT][hapmap]
rs2014810	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044571	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2376476	0.83[ASN][1000 genomes]
rs2376477	0.85[ASN][1000 genomes]
rs2889390	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs34221255	0.83[AMR][1000 genomes]
rs34630898	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35914913	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4494975	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4521287	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4679920	1.00[CEU][hapmap]
rs4679928	0.85[ASN][1000 genomes]
rs4679929	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4856700	0.80[CEU][hapmap]
rs57145341	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap]
rs6768115	1.00[CEU][hapmap]
rs6772723	0.90[CEU][hapmap]
rs6774725	1.00[CEU][hapmap]
rs6794882	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6801444	1.00[CEU][hapmap]
rs6806015	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68166680	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73021215	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73023235	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7433918	0.85[AMR][1000 genomes]
rs7610432	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611005	0.85[ASN][1000 genomes]
rs7618455	0.84[AMR][1000 genomes]
rs7618924	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7624185	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7628389	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7641892	1.00[CEU][hapmap]
rs898677	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs935497	1.00[CEU][hapmap]
rs956447	0.86[JPT][hapmap]
rs9812507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822435	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9832109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9844267	1.00[CEU][hapmap]
rs9845943	1.00[CEU][hapmap]
rs9857482	1.00[CEU][hapmap]
rs9857855	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9858335	0.81[CHB][hapmap]
rs9860537	1.00[CEU][hapmap]
rs9862086	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9880269	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9883566	0.90[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv965126	chr3:160748670-160750148	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs964533	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160748200-160749400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:160748800-160749200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:160748800-160749800	Enhancers	Liver	Liver
5	chr3:160748800-160749800	Enhancers	Placenta	Placenta

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