Variant report

Variant	rs7640874
Chromosome Location	chr3:160672617-160672618
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160672592..160674450-chr3:160676774..160679547,2	MCF-7	breast:
2	chr3:160670258..160673183-chr3:161089074..161090701,2	MCF-7	breast:
3	chr3:160671990..160674441-chr3:161088428..161090961,2	MCF-7	breast:
4	chr3:160666317..160670196-chr3:160671077..160673874,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10513558	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10513560	1.00[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs10936215	0.84[EUR][1000 genomes]
rs10936216	0.86[EUR][1000 genomes]
rs11709802	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12494673	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs12635022	0.85[ASN][1000 genomes]
rs12690576	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs13079792	0.85[ASN][1000 genomes]
rs13098529	0.84[EUR][1000 genomes]
rs1374787	0.83[CEU][hapmap]
rs1447608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1447609	0.86[EUR][1000 genomes]
rs1447624	0.87[JPT][hapmap]
rs1530636	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs1562465	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs1868104	0.86[JPT][hapmap]
rs1868108	0.83[CEU][hapmap]
rs1868109	0.83[CEU][hapmap]
rs2028988	0.86[JPT][hapmap]
rs2121721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2889391	0.86[EUR][1000 genomes]
rs34462546	0.86[EUR][1000 genomes]
rs4679667	0.80[JPT][hapmap]
rs4679925	0.86[ASN][1000 genomes]
rs6441343	0.86[ASN][1000 genomes]
rs6441344	0.86[ASN][1000 genomes]
rs6441345	0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs6441346	0.87[EUR][1000 genomes]
rs6763532	0.87[EUR][1000 genomes]
rs6770180	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6770488	0.80[JPT][hapmap]
rs6774203	1.00[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs6797498	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs6808386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs733948	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs745707	0.84[EUR][1000 genomes]
rs7610732	0.87[JPT][hapmap]
rs7613316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7616249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7626904	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626985	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778651	0.81[JPT][hapmap]
rs878954	0.82[ASN][1000 genomes]
rs878955	0.82[ASN][1000 genomes]
rs898682	0.88[CEU][hapmap]
rs956447	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs9813700	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9840600	0.92[CEU][hapmap]
rs9846254	0.92[CEU][hapmap]
rs9857743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9860182	0.96[CEU][hapmap]
rs9881807	0.83[CEU][hapmap]

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	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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7640874	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160666400-160673400	Weak transcription	Right Atrium	heart
2	chr3:160667400-160696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:160670200-160686600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:160670400-160686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:160670600-160682200	Weak transcription	Left Ventricle	heart
7	chr3:160672400-160674200	Weak transcription	Fetal Brain Female	brain

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