Variant report

Variant	rs2622274
Chromosome Location	chr6:64240516-64240517
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:64234904..64241405-chr6:64279564..64285170,9	MCF-7	breast:
2	chr6:64232325..64242084-chr6:64281113..64285530,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112245	Chromatin interaction
ENSG00000266680	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10943822	0.82[ASN][1000 genomes]
rs10943823	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10943902	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11756357	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11759194	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1197897	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1197898	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1197901	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197904	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1197905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1211293	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212827	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196062	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12213364	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13206102	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1322411	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322412	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322413	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1322415	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322416	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1570314	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1570315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1570316	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1612517	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1615166	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1620671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1622589	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1630182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1631580	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1681932	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1681940	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1681941	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1681942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681944	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1681945	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681948	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1681957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744133	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1744134	0.83[TSI][hapmap]
rs1744135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1744137	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1744138	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1744140	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1744141	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744142	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744144	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744145	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1744146	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744148	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744149	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1744152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1744155	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1744158	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1744161	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1779742	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1779765	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779766	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779767	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779769	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779770	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779771	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779772	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779773	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779774	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1779775	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1779779	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779782	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1872289	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076874	0.83[JPT][hapmap]
rs2146149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146151	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146152	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2186011	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2250179	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2448774	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2622276	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622280	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622282	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622283	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622284	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622285	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622293	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622294	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622297	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622298	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2622299	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622300	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2622304	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2758225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2758226	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2758228	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758229	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2758230	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2758231	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758232	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2758233	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2758234	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758235	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2758236	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758238	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758242	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758247	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2758248	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2758250	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2758259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2800038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800044	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2800045	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2800047	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2800048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2800049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2800050	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2800051	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2800052	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2928873	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2984458	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4299811	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4358600	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4482958	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4521569	0.80[ASN][1000 genomes]
rs4538688	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4543353	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4557499	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4710430	0.87[EUR][1000 genomes]
rs4710431	0.81[EUR][1000 genomes]
rs6454235	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454236	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6454244	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6924479	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6938965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6939324	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6939983	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6942342	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs733912	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7738916	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7742595	0.85[EUR][1000 genomes]
rs7745873	0.87[EUR][1000 genomes]
rs7773557	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7774196	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294229	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294269	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs9341893	0.81[EUR][1000 genomes]
rs9344168	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9344188	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9350929	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353015	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9353016	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9353017	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9353023	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9361779	0.85[EUR][1000 genomes]
rs9361827	0.80[ASN][1000 genomes]
rs9361829	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9361838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9361844	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9443919	0.81[EUR][1000 genomes]
rs9443921	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9443931	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9449291	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs9449297	0.85[EUR][1000 genomes]
rs9449312	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2622274	LGSN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64237000-64240600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:64238400-64241000	Genic enhancers	HepG2	liver
3	chr6:64239200-64240600	Flanking Active TSS	Hela-S3	cervix
4	chr6:64239800-64241200	Enhancers	HMEC	breast
5	chr6:64239800-64243800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:64240400-64240600	Enhancers	NHEK	skin
7	chr6:64240400-64241000	Active TSS	A549	lung
8	chr6:64240400-64241200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:64240400-64245600	Weak transcription	Liver	Liver
10	chr6:64240400-64254000	Weak transcription	Psoas Muscle	Psoas

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