Variant report

Variant	rs2725830
Chromosome Location	chr11:77141718-77141719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77140271..77141778-chr11:77152557..77155185,2	MCF-7	breast:
2	chr11:77139694..77142653-chr11:77149124..77150876,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10793248	0.85[ASN][1000 genomes]
rs10899376	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs10899378	0.97[EUR][1000 genomes]
rs10899379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11237173	0.95[EUR][1000 genomes]
rs11237189	0.96[EUR][1000 genomes]
rs11237193	0.97[EUR][1000 genomes]
rs11237195	0.90[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs11237196	0.95[EUR][1000 genomes]
rs11237199	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs12271542	0.95[EUR][1000 genomes]
rs12420360	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs1377470	0.95[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs1377471	0.94[EUR][1000 genomes]
rs1453343	0.88[EUR][1000 genomes]
rs1670459	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1793476	0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs1793483	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1840151	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250639	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2250647	0.95[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2298793	0.95[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2602458	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602459	0.93[EUR][1000 genomes]
rs2602460	0.81[AFR][1000 genomes]
rs2602462	0.86[AFR][1000 genomes]
rs2602463	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602464	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2602465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2602468	0.94[EUR][1000 genomes]
rs2602469	0.94[EUR][1000 genomes]
rs2602470	0.94[EUR][1000 genomes]
rs2602472	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602473	0.89[YRI][hapmap]
rs2602477	0.98[EUR][1000 genomes]
rs2602479	0.98[EUR][1000 genomes]
rs2602488	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2602489	0.88[EUR][1000 genomes]
rs2725810	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2725812	0.82[JPT][hapmap]
rs2725815	0.88[EUR][1000 genomes]
rs2725816	0.94[EUR][1000 genomes]
rs2725826	0.88[EUR][1000 genomes]
rs2725827	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2725831	0.94[EUR][1000 genomes]
rs2725832	0.93[EUR][1000 genomes]
rs2729747	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729753	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2729762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2729769	0.88[EUR][1000 genomes]
rs2729771	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844328	0.98[EUR][1000 genomes]
rs2844332	0.98[EUR][1000 genomes]
rs2844333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844334	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2844336	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844337	0.95[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2852383	0.81[AFR][1000 genomes]
rs2852384	0.98[EUR][1000 genomes]
rs2852385	0.93[EUR][1000 genomes]
rs2852388	0.86[YRI][hapmap]
rs2852389	0.89[AFR][1000 genomes]
rs2852390	0.95[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs2852392	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2852394	0.98[EUR][1000 genomes]
rs2853086	0.97[EUR][1000 genomes]
rs2853087	0.98[EUR][1000 genomes]
rs2853088	0.96[EUR][1000 genomes]
rs2853090	0.94[EUR][1000 genomes]
rs2853103	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs3015984	0.83[ASN][1000 genomes]
rs3015989	0.95[JPT][hapmap]
rs3015993	0.95[JPT][hapmap]
rs3019240	0.83[ASN][1000 genomes]
rs3019258	0.85[ASN][1000 genomes]
rs4590893	0.94[EUR][1000 genomes]
rs476925	0.87[JPT][hapmap]
rs478475	0.80[ASN][1000 genomes]
rs4945162	0.83[JPT][hapmap]
rs4945166	0.83[JPT][hapmap]
rs495889	0.95[JPT][hapmap]
rs514191	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs575662	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs599437	0.87[JPT][hapmap]
rs628325	0.85[ASN][1000 genomes]
rs6592721	0.89[AFR][1000 genomes]
rs674652	0.95[JPT][hapmap]
rs683497	0.85[ASN][1000 genomes]
rs688212	0.87[JPT][hapmap]
rs7109645	0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs7112264	0.88[AFR][1000 genomes]
rs7118869	0.87[JPT][hapmap]
rs7119033	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7943778	0.85[EUR][1000 genomes]
rs947809	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2725830	UCP2	cis	cerebellum	SCAN
rs2725830	RELT	cis	cerebellum	SCAN
rs2725830	PAK1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77123400-77147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:77123400-77147200	Weak transcription	Pancreas	Pancrea
3	chr11:77124200-77147000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:77130000-77147000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:77130200-77143000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:77131400-77147000	Weak transcription	Fetal Intestine Small	intestine
7	chr11:77132400-77145600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr11:77134000-77141800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:77135400-77149000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:77138800-77146800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:77139000-77142600	Weak transcription	GM12878-XiMat	blood
12	chr11:77139200-77142000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:77139200-77144200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:77140000-77142000	Weak transcription	Gastric	stomach
15	chr11:77141000-77146200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr11:77141400-77141800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:77141600-77148600	Weak transcription	Ovary	ovary

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