Variant report

Variant	rs2248930
Chromosome Location	chr5:112811119-112811120
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112810517..112812922-chr5:112822746..112824513,2	MCF-7	breast:
2	chr5:112809363..112813589-chr5:112821986..112825015,5	MCF-7	breast:
3	chr5:112811062..112815504-chr5:112818708..112822151,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10038521	0.86[CHB][hapmap]
rs10040430	0.80[AFR][1000 genomes]
rs10046057	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs10061462	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs10062004	0.86[JPT][hapmap]
rs10065790	0.86[CHB][hapmap];0.81[MEX][hapmap]
rs10071684	0.86[CHB][hapmap]
rs10077431	0.86[CHB][hapmap];0.81[MEX][hapmap]
rs10078214	0.86[CHB][hapmap]
rs10434754	0.86[CHB][hapmap]
rs1057827	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241210	0.80[AFR][1000 genomes]
rs13159509	0.86[CHB][hapmap]
rs13164326	0.86[CHB][hapmap]
rs13170435	0.86[CHB][hapmap]
rs13174075	0.86[CHB][hapmap]
rs13174206	0.86[CHB][hapmap]
rs13180516	0.86[CHB][hapmap]
rs13181534	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs13181732	0.86[CHB][hapmap]
rs13182972	0.86[CHB][hapmap]
rs13183383	0.86[CHB][hapmap]
rs13184538	0.86[CHB][hapmap]
rs13188946	0.81[GIH][hapmap]
rs13189050	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs1366393	0.81[GIH][hapmap]
rs1643824	0.82[EUR][1000 genomes]
rs168365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs168366	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171180	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17325307	0.86[CHB][hapmap]
rs17325825	0.86[CHB][hapmap]
rs17327964	0.86[CHB][hapmap]
rs17331844	0.86[CHB][hapmap]
rs17388260	0.86[CHB][hapmap]
rs17389165	0.86[CHB][hapmap]
rs1838206	0.85[CHB][hapmap]
rs1850407	0.81[GIH][hapmap]
rs191553	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965429	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs255860	0.86[EUR][1000 genomes]
rs26959	0.81[GIH][hapmap]
rs26991	0.89[YRI][hapmap]
rs27567	0.81[GIH][hapmap]
rs28785806	0.89[EUR][1000 genomes]
rs28848005	0.80[AFR][1000 genomes]
rs3097242	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs348924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348926	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs348928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs348932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348938	0.81[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348940	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348941	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs348945	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348946	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348948	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348951	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348952	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348954	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348957	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348958	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348960	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348961	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs348962	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348963	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs364738	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366219	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs367943	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3842917	1.00[YRI][hapmap]
rs388363	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4438866	0.82[CHB][hapmap]
rs444322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs451425	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451453	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs455435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs458044	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs460079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs463167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs463249	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4705821	1.00[YRI][hapmap]
rs4705823	1.00[YRI][hapmap]
rs4705827	0.82[YRI][hapmap]
rs644154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6594707	0.89[JPT][hapmap]
rs6594713	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6594714	0.86[CHB][hapmap]
rs6594718	0.95[YRI][hapmap]
rs6594721	1.00[YRI][hapmap]
rs6594732	0.82[YRI][hapmap]
rs6594733	0.82[YRI][hapmap]
rs6867397	0.81[GIH][hapmap]
rs6867579	0.86[CHB][hapmap]
rs6870401	0.86[CHB][hapmap]
rs6871934	0.86[CHB][hapmap]
rs6874175	0.86[CHB][hapmap]
rs6883102	0.85[CHB][hapmap]
rs6883547	0.86[CHB][hapmap]
rs6887482	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6887816	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6887914	0.86[CHB][hapmap]
rs6890874	0.86[CHB][hapmap]
rs7701895	0.86[CHB][hapmap]
rs7706721	0.86[CHB][hapmap]
rs7709110	1.00[YRI][hapmap]
rs7709646	0.85[CHB][hapmap]
rs7714760	0.86[CHB][hapmap]
rs7718203	0.85[CHB][hapmap]
rs7718616	0.86[CHB][hapmap]
rs7729269	0.86[CHB][hapmap]
rs7730801	0.96[YRI][hapmap]
rs8180416	0.86[CHB][hapmap]
rs929774	0.81[YRI][hapmap]
rs9326884	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs9326890	0.86[CHB][hapmap];0.81[MEX][hapmap]
rs9632462	0.89[JPT][hapmap]
rs9687443	0.83[EUR][1000 genomes]
rs9800375	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112807800-112821600	Weak transcription	HMEC	breast
2	chr5:112808800-112812400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112810200-112811200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:112810200-112811600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:112810200-112823000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:112810400-112820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:112810400-112821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:112810600-112813200	Weak transcription	Fetal Heart	heart
9	chr5:112811000-112811800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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