Variant report

Variant	rs1541346
Chromosome Location	chr17:59694919-59694920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:53297685..53299225-chr17:59694461..59696347,2	MCF-7	breast:
2	chr17:59693752..59696343-chr17:59703736..59707002,4	MCF-7	breast:
3	chr17:59694214..59697045-chr17:59717627..59720689,3	MCF-7	breast:
4	chr17:59694658..59695552-chr20:45824679..45825551,2	MCF-7	breast:
5	chr17:59692941..59695723-chr17:59718310..59720585,2	K562	blood:

Variant related genes	Relation type
ENSG00000170421	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1015771	0.95[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10221278	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10438771	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];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10468558	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[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10515206	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515207	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515211	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs10853038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10853039	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079448	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11650471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651510	0.86[EUR][1000 genomes]
rs11871753	0.90[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs12449319	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12449902	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12449934	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12450027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451862	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs12453293	0.85[EUR][1000 genomes]
rs12453801	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[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453966	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs12603485	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12603617	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12937232	0.80[EUR][1000 genomes]
rs12949659	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs1468577	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs16945500	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17532528	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17610705	0.81[YRI][hapmap]
rs1978244	0.90[CEU][hapmap];0.83[TSI][hapmap]
rs1990338	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs2040608	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2158006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191249	0.95[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2214184	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2378874	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378875	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378884	0.84[EUR][1000 genomes]
rs2378905	0.90[CEU][hapmap]
rs2890012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2890013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2890021	0.95[CEU][hapmap]
rs36031690	0.82[EUR][1000 genomes]
rs4309463	0.80[EUR][1000 genomes]
rs4343344	0.80[EUR][1000 genomes]
rs4580256	0.85[EUR][1000 genomes]
rs4968444	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968447	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs4968577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968580	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968582	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[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4968584	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968585	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968588	0.80[EUR][1000 genomes]
rs55797010	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55944442	0.94[ASN][1000 genomes]
rs56284136	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57099937	0.85[EUR][1000 genomes]
rs57393813	0.85[EUR][1000 genomes]
rs61599541	0.84[EUR][1000 genomes]
rs62070615	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62070616	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62070617	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62070624	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6504066	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs6504068	0.95[CEU][hapmap]
rs6504071	0.94[CEU][hapmap]
rs6504072	0.90[CEU][hapmap]
rs67273191	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67938055	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717961	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs717962	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs7207074	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs7207881	0.95[CEU][hapmap]
rs7208704	0.94[CEU][hapmap]
rs7212172	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7212423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs7213329	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7213470	0.80[EUR][1000 genomes]
rs7213587	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs7213759	0.84[EUR][1000 genomes]
rs7214884	0.87[CEU][hapmap]
rs7215784	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7216756	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7217206	0.94[CEU][hapmap]
rs7220688	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs7220719	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs7222799	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs72841508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075370	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs8078977	0.84[CEU][hapmap]
rs8182296	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9303449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9807012	0.90[EUR][1000 genomes]
rs9895987	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs9896013	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897121	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs9897450	0.80[EUR][1000 genomes]
rs9897928	0.95[CEU][hapmap]
rs9901428	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9902995	0.95[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9903041	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9904292	0.90[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs9904294	0.80[EUR][1000 genomes]
rs9905870	0.83[EUR][1000 genomes]
rs9906313	0.95[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9907299	0.89[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541346	BRIP1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59693400-59695200	Enhancers	Fetal Lung	lung
2	chr17:59693600-59701200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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