Variant report

Variant	rs1868109
Chromosome Location	chr3:160682500-160682501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160680508..160683340-chr3:160683641..160685438,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10154889	0.84[JPT][hapmap]
rs10433352	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10513560	0.83[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10936215	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10936216	0.81[EUR][1000 genomes]
rs11711152	0.81[JPT][hapmap]
rs11718966	0.81[JPT][hapmap]
rs11922296	0.90[JPT][hapmap]
rs12690576	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs13071999	0.81[JPT][hapmap]
rs13073059	0.81[JPT][hapmap]
rs13098529	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1348976	0.90[JPT][hapmap]
rs1374787	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1374789	0.90[JPT][hapmap]
rs1374790	0.89[JPT][hapmap]
rs1374795	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs1447608	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs1447609	0.81[EUR][1000 genomes]
rs1447610	0.81[JPT][hapmap]
rs1447615	0.90[JPT][hapmap]
rs1447622	0.90[JPT][hapmap]
rs1447626	0.95[CEU][hapmap]
rs1530636	0.83[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1562464	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1562465	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1580254	0.95[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs16831796	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs1839018	0.90[JPT][hapmap]
rs1868107	0.81[JPT][hapmap]
rs1868108	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs2044571	0.85[JPT][hapmap]
rs2121721	0.83[CEU][hapmap];0.81[CHD][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2376476	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2376477	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2889391	0.81[EUR][1000 genomes]
rs34462546	0.81[EUR][1000 genomes]
rs34884182	0.85[EUR][1000 genomes]
rs4679920	0.85[JPT][hapmap]
rs4679928	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6441338	0.81[JPT][hapmap]
rs6441345	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs6441346	0.82[EUR][1000 genomes]
rs6763532	0.82[EUR][1000 genomes]
rs6768115	0.81[JPT][hapmap]
rs6769927	0.82[EUR][1000 genomes]
rs6770180	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6774203	0.83[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs6774725	0.81[JPT][hapmap]
rs6791375	0.85[EUR][1000 genomes]
rs6801330	0.90[JPT][hapmap]
rs6808311	0.84[EUR][1000 genomes]
rs6808386	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs733948	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs745707	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7611005	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7613316	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs7616249	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs7628389	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs7635796	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs7640874	0.83[CEU][hapmap]
rs7641892	0.81[JPT][hapmap]
rs7644586	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs898677	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs935497	0.81[JPT][hapmap]
rs956447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs964533	0.90[JPT][hapmap]
rs9812507	0.90[JPT][hapmap]
rs9813700	0.85[EUR][1000 genomes]
rs9832109	0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs9839984	0.95[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9844267	0.81[JPT][hapmap]
rs9846254	0.82[TSI][hapmap]
rs9857482	0.80[JPT][hapmap]
rs9857743	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs9857855	0.90[JPT][hapmap]
rs9858335	0.95[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9860182	0.82[TSI][hapmap]
rs9873705	0.85[EUR][1000 genomes]
rs9881807	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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
3	esv3462791	chr3:160680085-160686174	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3462792	chr3:160680137-160686148	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3462790	chr3:160680198-160686110	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3462793	chr3:160680198-160686110	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv16422	chr3:160680271-160685991	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv592129	chr3:160681614-160684597	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv517658	chr3:160681614-160684720	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv592130	chr3:160681614-160685894	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv592131	chr3:160682296-160685788	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv592132	chr3:160682296-160685894	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv592133	chr3:160682500-160685753	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv592134	chr3:160682500-160685894	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv592135	chr3:160682500-160689164	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1868109	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160667400-160696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:160670200-160686600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:160670400-160686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:160678400-160697600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:160679000-160686600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:160680000-160683600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:160680000-160684400	Weak transcription	Dnd41	blood
9	chr3:160681000-160686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:160681600-160684800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:160682400-160686600	Weak transcription	Left Ventricle	heart

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