Variant report

Variant	rs7616988
Chromosome Location	chr3:99701134-99701135
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	chr3:99699563..99701368-chr3:99701807..99704469,2	MCF-7	breast:
2	chr3:99693171..99696076-chr3:99698445..99701698,3	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10049383	0.94[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1016914	0.82[JPT][hapmap]
rs1017968	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1021102	0.81[JPT][hapmap]
rs1021103	0.94[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10212525	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1021341	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap]
rs1038294	0.87[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10511177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1087198	0.82[JPT][hapmap]
rs10936005	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs10936008	0.91[ASW][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1287283	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap]
rs13064704	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs13069311	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs13317017	0.82[JPT][hapmap]
rs13323143	0.94[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1489816	0.94[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap]
rs1688766	0.94[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1688771	0.94[CEU][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1688772	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1688782	0.81[GIH][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs1718246	0.81[EUR][1000 genomes]
rs17379739	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17392948	0.87[CEU][hapmap];0.81[GIH][hapmap]
rs17393059	0.81[EUR][1000 genomes]
rs2452320	0.82[JPT][hapmap]
rs2452321	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs28714363	0.83[EUR][1000 genomes]
rs35521705	0.83[EUR][1000 genomes]
rs4075038	0.94[CEU][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244711	0.82[JPT][hapmap]
rs4279135	0.83[EUR][1000 genomes]
rs4361315	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap]
rs4479633	0.82[JPT][hapmap]
rs4571265	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4928149	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs4928232	0.82[JPT][hapmap]
rs4928234	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6440938	0.82[JPT][hapmap]
rs6765027	0.82[JPT][hapmap]
rs6790535	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs6790877	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs6799379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6802422	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs6806178	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6807176	1.00[ASW][hapmap];0.94[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs6809988	0.82[JPT][hapmap]
rs704581	0.91[YRI][hapmap]
rs704582	0.94[CEU][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs704583	0.82[JPT][hapmap]
rs7609729	1.00[JPT][hapmap]
rs7610486	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7620228	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs7627991	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs7629426	0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7636447	0.82[JPT][hapmap]
rs7638900	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs793440	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs793445	0.82[JPT][hapmap]
rs793452	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap]
rs793453	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap]
rs793457	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793460	0.82[JPT][hapmap]
rs793461	0.82[JPT][hapmap]
rs793462	0.82[JPT][hapmap]
rs793463	0.82[JPT][hapmap]
rs793465	0.82[JPT][hapmap]
rs793466	0.82[JPT][hapmap]
rs793467	0.82[JPT][hapmap]
rs793468	0.82[JPT][hapmap]
rs793470	0.82[JPT][hapmap]
rs793472	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793474	0.81[GIH][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs793492	0.81[ASN][1000 genomes]
rs793494	0.82[JPT][hapmap]
rs793495	0.82[JPT][hapmap]
rs793496	0.94[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793499	0.94[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793503	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs796977	0.90[JPT][hapmap]
rs796978	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs809415	0.82[JPT][hapmap]
rs812657	0.82[JPT][hapmap]
rs923470	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs923471	0.94[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs9810235	0.83[EUR][1000 genomes]
rs9814359	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs9815439	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs9823908	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs9828079	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs9832186	0.83[EUR][1000 genomes]
rs9833888	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9833980	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs9834484	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9837602	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs9841186	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs9851645	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs9852435	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9853823	0.86[EUR][1000 genomes]
rs9854260	0.81[CEU][hapmap]
rs9860290	0.81[CEU][hapmap]
rs9864437	0.94[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs9872871	0.82[JPT][hapmap]
rs9873709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9873878	0.94[CEU][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9875640	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9875664	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9878931	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7616988	FILIP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99689800-99702000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99697600-99701200	Weak transcription	Fetal Intestine Small	intestine
3	chr3:99697800-99709200	Weak transcription	Psoas Muscle	Psoas
4	chr3:99700200-99703200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:99700400-99701400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:99700800-99701400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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