Variant report

Variant	rs4679920
Chromosome Location	chr3:160612349-160612350
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

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[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713093	0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs11717272	0.90[CEU][hapmap]
rs11718966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11916355	0.84[EUR][1000 genomes]
rs11922296	0.86[JPT][hapmap]
rs13071999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13073059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13256	0.90[CEU][hapmap]
rs13315565	0.94[CEU][hapmap]
rs1345156	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1348976	0.86[JPT][hapmap]
rs1374789	0.86[JPT][hapmap]
rs1374790	0.86[JPT][hapmap]
rs1374795	0.81[JPT][hapmap]
rs1447610	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1447615	0.86[JPT][hapmap]
rs1447622	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1562464	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs16831563	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831796	0.81[CEU][hapmap]
rs1839016	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839018	0.85[JPT][hapmap]
rs1868105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1868107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868109	0.85[JPT][hapmap]
rs2044571	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2197700	0.85[EUR][1000 genomes]
rs2889390	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs35257491	0.85[EUR][1000 genomes]
rs6441337	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66872845	0.82[EUR][1000 genomes]
rs6768115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6774725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801330	0.85[JPT][hapmap]
rs6801444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7624185	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs7628389	0.81[CEU][hapmap]
rs7641892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs898677	0.81[CEU][hapmap]
rs935497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs956447	0.86[JPT][hapmap]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs9822435	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs9832109	1.00[CEU][hapmap]
rs9844267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845943	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]
rs9857482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9857855	0.85[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9871801	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap]
rs9883566	0.90[CEU][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3391648	chr3:160602299-160620598	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679920	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160604400-160616600	Weak transcription	Psoas Muscle	Psoas
2	chr3:160610800-160612400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:160611200-160615200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160611200-160619400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:160611400-160615200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:160611600-160615400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:160611600-160615400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:160611600-160618600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:160612200-160612400	Enhancers	Fetal Brain Male	brain
10	chr3:160612200-160614600	Weak transcription	Fetal Brain Female	brain
11	chr3:160612200-160615400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:160612200-160618800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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