Variant report

Variant	rs684773
Chromosome Location	chr3:135956305-135956306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135953105..135954994-chr3:135955237..135956991,2	MCF-7	breast:
2	chr3:135954886..135956782-chr3:136102988..136105563,2	MCF-7	breast:
3	chr3:135955194..135957382-chr3:135967889..135969974,2	MCF-7	breast:
4	chr3:135914260..135917175-chr3:135955428..135961207,5	MCF-7	breast:
5	chr3:135954969..135958105-chr3:135968052..135971178,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction
ENSG00000114054	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10935177	1.00[JPT][hapmap]
rs10935182	0.81[JPT][hapmap]
rs10935184	0.86[JPT][hapmap]
rs1145101	0.94[MEX][hapmap];0.88[MKK][hapmap]
rs1145106	0.81[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs1153870	0.93[ASN][1000 genomes]
rs1153871	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153872	0.95[ASN][1000 genomes]
rs1153877	0.86[JPT][hapmap]
rs1154988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12330635	0.88[CHB][hapmap]
rs1278493	1.00[JPT][hapmap]
rs1278719	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1279086	0.86[JPT][hapmap]
rs1279425	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1279831	1.00[JPT][hapmap]
rs1279840	0.84[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs1711171	0.82[ASW][hapmap];0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs17252498	0.83[CEU][hapmap];0.88[MEX][hapmap]
rs2655008	0.81[JPT][hapmap]
rs3755636	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772390	1.00[CHB][hapmap]
rs3821445	0.88[CEU][hapmap];0.94[MEX][hapmap]
rs3957816	1.00[JPT][hapmap]
rs4678428	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs483465	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs518972	0.86[JPT][hapmap]
rs523118	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs534944	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548288	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556788	0.86[JPT][hapmap]
rs571513	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs576771	0.84[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs589092	0.86[JPT][hapmap]
rs606725	0.84[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs610860	0.88[CEU][hapmap]
rs61789601	0.86[EUR][1000 genomes]
rs61791757	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs619605	0.81[JPT][hapmap]
rs632016	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs645040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs650326	0.86[JPT][hapmap]
rs650505	0.83[ASN][1000 genomes]
rs654237	0.81[JPT][hapmap]
rs655836	0.81[JPT][hapmap]
rs661739	1.00[JPT][hapmap]
rs665200	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs667920	0.86[JPT][hapmap];0.88[MEX][hapmap]
rs6779146	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs687339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs695983	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs696081	0.86[JPT][hapmap]
rs696516	0.90[ASW][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs696517	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs696518	0.81[JPT][hapmap]
rs696520	0.86[JPT][hapmap]
rs698270	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs72493178	0.85[ASN][1000 genomes]
rs73222262	0.83[ASN][1000 genomes]
rs7372313	1.00[JPT][hapmap]
rs7628146	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8045	0.82[MEX][hapmap]
rs895893	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs895894	1.00[JPT][hapmap]
rs9810089	0.86[JPT][hapmap]
rs9811753	0.85[JPT][hapmap]
rs9840812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9845457	1.00[JPT][hapmap]
rs9848883	0.88[CHB][hapmap]
rs9856769	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2760738	chr3:135943988-135957333	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs684773	MSL2	cis	cerebellum	SCAN
rs684773	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135954600-135958400	Enhancers	HepG2	liver
2	chr3:135955000-135956600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:135955000-135956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:135955200-135956400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:135955800-135956600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:135955800-135957000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:135955800-135958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:135956000-135956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:135956000-135957800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr3:135956000-135958200	Enhancers	Liver	Liver

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