Variant report

Variant	rs9449295
Chromosome Location	chr6:64163807-64163808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:64162095..64163883-chr6:64281750..64283418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112245	Chromatin interaction
ENSG00000266680	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10806215	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10943823	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11756357	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11759194	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12196062	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12213364	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13206102	0.83[EUR][1000 genomes]
rs1322411	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1322412	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1322413	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1570314	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1570315	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1570316	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1612517	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1615166	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1620671	0.81[EUR][1000 genomes]
rs1622589	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1630182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1631580	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1681932	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1681940	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1681941	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1681944	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1681946	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1681947	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1681948	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1681957	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744133	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1744135	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1744137	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1744138	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744140	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1744141	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744142	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744144	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744145	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1744146	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744147	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1744148	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1744152	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1744158	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1744161	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779742	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1779765	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779766	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779767	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779769	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779770	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779771	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779772	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779773	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1779774	0.82[EUR][1000 genomes]
rs1779775	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1779779	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1872289	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2146149	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2146150	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2146151	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2146152	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2186011	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2250179	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2448774	0.83[EUR][1000 genomes]
rs2622276	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2622280	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2622281	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622282	0.87[AMR][1000 genomes]
rs2622283	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622284	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622285	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622293	0.80[AMR][1000 genomes]
rs2622297	0.82[AMR][1000 genomes]
rs2622298	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2622299	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622300	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622304	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2758224	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758225	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758226	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758228	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2758229	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2758230	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2758231	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758232	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758233	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758234	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2758235	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2758236	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2758237	0.81[EUR][1000 genomes]
rs2758238	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2758247	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758248	0.82[AMR][1000 genomes]
rs2758250	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2758259	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2800044	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2800045	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2800047	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2800048	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2800049	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2800050	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2800051	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2800052	0.82[EUR][1000 genomes]
rs2928873	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2984458	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4299811	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4482958	0.83[EUR][1000 genomes]
rs4557499	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4710430	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4710431	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6454235	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6454236	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6454244	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6924479	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6938965	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6939324	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6939983	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6942342	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs733912	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7738916	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7742595	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7745873	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7773557	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9294229	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9294234	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9341893	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9344168	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9344188	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9350929	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9353004	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9353015	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9353016	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9353017	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9353023	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9359467	0.81[AMR][1000 genomes]
rs9361762	0.81[AMR][1000 genomes]
rs9361767	0.81[AMR][1000 genomes]
rs9361779	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9361816	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9361827	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9361829	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9361838	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9361844	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9443919	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9443921	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9443931	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9449291	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9449297	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9449312	0.83[AMR][1000 genomes];0.86[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	nsv1019831	chr6:63279677-64230736	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9449295	LGSN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64158000-64168200	Enhancers	HepG2	liver
2	chr6:64158400-64168400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:64162200-64164000	Active TSS	Liver	Liver
4	chr6:64162400-64166400	Weak transcription	Pancreas	Pancrea
5	chr6:64162400-64166800	Weak transcription	Stomach Mucosa	stomach
6	chr6:64162800-64164400	Enhancers	A549	lung
7	chr6:64162800-64167600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:64163000-64166400	Weak transcription	Fetal Intestine Large	intestine
9	chr6:64163400-64168600	Weak transcription	Hela-S3	cervix

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