Variant report

Variant	rs9845943
Chromosome Location	chr3:160635849-160635850
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160620374..160622809-chr3:160634406..160636878,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap]
rs10433352	0.81[CEU][hapmap]
rs11711152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713093	0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.90[GIH][hapmap]
rs11718966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11916355	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13071999	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13256	0.90[CEU][hapmap];0.93[GIH][hapmap]
rs13315565	0.94[CEU][hapmap]
rs1345156	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1447610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1447622	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1562464	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs16831563	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs1839016	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1868105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1868108	0.82[CHD][hapmap]
rs2044571	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs2889390	0.81[JPT][hapmap]
rs4521287	0.90[CEU][hapmap];0.90[GIH][hapmap]
rs4679920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441337	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66872845	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6774725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6801444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7624185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs7628389	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs7641892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898677	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs935497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap]
rs9822435	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs9832109	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs9844267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9857482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9857855	0.84[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs9871801	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.93[GIH][hapmap]
rs9881807	0.86[CHD][hapmap];0.80[GIH][hapmap]
rs9883566	0.90[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9845943	B3GALNT1	cis	lymphoblastoid	seeQTL
rs9845943	SPTSSB	cis	Thyroid	GTEx
rs9845943	C3orf57	cis	parietal	SCAN
rs9845943	PPM1L	cis	cerebellum	SCAN
rs9845943	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160630200-160641400	Weak transcription	Psoas Muscle	Psoas
2	chr3:160634600-160636000	Enhancers	Fetal Brain Male	brain
3	chr3:160635400-160644000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:160635400-160649200	Weak transcription	Fetal Brain Female	brain
5	chr3:160635800-160636000	Enhancers	Skeletal Muscle Female	skeletal muscle

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