Variant report

Variant	rs9352960
Chromosome Location	chr6:64150426-64150427
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:64150213-64150450	A549	lung:	n/a	n/a
2	MAX	chr6:64149902-64150712	A549	lung:	n/a	n/a
3	REST	chr6:64150025-64150974	A549	lung:	n/a	n/a
4	POLR2A	chr6:64150079-64150779	A549	lung:	n/a	n/a
5	TAF1	chr6:64149908-64150650	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000218048	TF binding region

Extended variants
information (count: 187 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:186)

rs_ID	r²[population]
rs10755410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10806206	0.84[EUR][1000 genomes]
rs10806215	0.93[ASN][1000 genomes]
rs10943823	0.82[ASN][1000 genomes]
rs11756357	0.82[ASN][1000 genomes]
rs11759194	0.88[ASN][1000 genomes]
rs1197898	0.82[ASN][1000 genomes]
rs1197901	0.81[ASN][1000 genomes]
rs1197902	0.81[ASN][1000 genomes]
rs1197904	0.82[ASN][1000 genomes]
rs1197905	0.82[ASN][1000 genomes]
rs1212827	0.82[ASN][1000 genomes]
rs12196062	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12213364	0.88[ASN][1000 genomes]
rs13206102	0.85[ASN][1000 genomes]
rs1322411	0.82[ASN][1000 genomes]
rs1322412	0.82[ASN][1000 genomes]
rs1322413	0.82[ASN][1000 genomes]
rs1570314	0.82[ASN][1000 genomes]
rs1570315	0.82[ASN][1000 genomes]
rs1570316	0.82[ASN][1000 genomes]
rs1612517	0.83[ASN][1000 genomes]
rs1615166	0.83[ASN][1000 genomes]
rs1620671	0.82[ASN][1000 genomes]
rs1622589	0.82[ASN][1000 genomes]
rs1630182	0.82[ASN][1000 genomes]
rs1681932	0.85[ASN][1000 genomes]
rs1681940	0.82[ASN][1000 genomes]
rs1681941	0.82[ASN][1000 genomes]
rs1681944	0.83[ASN][1000 genomes]
rs1681945	0.82[ASN][1000 genomes]
rs1681946	0.82[ASN][1000 genomes]
rs1681947	0.82[ASN][1000 genomes]
rs1681948	0.85[ASN][1000 genomes]
rs1681957	0.82[ASN][1000 genomes]
rs1723535	0.80[EUR][1000 genomes]
rs1741801	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1744133	0.83[ASN][1000 genomes]
rs1744135	0.83[ASN][1000 genomes]
rs1744137	0.82[ASN][1000 genomes]
rs1744138	0.81[ASN][1000 genomes]
rs1744140	0.82[ASN][1000 genomes]
rs1744141	0.82[ASN][1000 genomes]
rs1744142	0.82[ASN][1000 genomes]
rs1744144	0.82[ASN][1000 genomes]
rs1744145	0.81[ASN][1000 genomes]
rs1744146	0.82[ASN][1000 genomes]
rs1744147	0.82[ASN][1000 genomes]
rs1744148	0.82[ASN][1000 genomes]
rs1744149	0.82[ASN][1000 genomes]
rs1744152	0.85[ASN][1000 genomes]
rs1744158	0.85[ASN][1000 genomes]
rs1744161	0.85[ASN][1000 genomes]
rs1779747	0.80[EUR][1000 genomes]
rs1779765	0.82[ASN][1000 genomes]
rs1779766	0.82[ASN][1000 genomes]
rs1779767	0.82[ASN][1000 genomes]
rs1779769	0.82[ASN][1000 genomes]
rs1779770	0.82[ASN][1000 genomes]
rs1779771	0.82[ASN][1000 genomes]
rs1779772	0.82[ASN][1000 genomes]
rs1779773	0.82[ASN][1000 genomes]
rs1779774	0.81[ASN][1000 genomes]
rs1779775	0.82[ASN][1000 genomes]
rs1779779	0.82[ASN][1000 genomes]
rs1872289	0.82[ASN][1000 genomes]
rs1969717	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2076874	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2096346	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2146149	0.85[ASN][1000 genomes]
rs2146150	0.85[ASN][1000 genomes]
rs2146151	0.85[ASN][1000 genomes]
rs2146152	0.85[ASN][1000 genomes]
rs2186011	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2250179	0.91[ASN][1000 genomes]
rs2448774	0.85[ASN][1000 genomes]
rs2622276	0.87[ASN][1000 genomes]
rs2622280	0.83[ASN][1000 genomes]
rs2622281	0.85[ASN][1000 genomes]
rs2622282	0.83[ASN][1000 genomes]
rs2622283	0.85[ASN][1000 genomes]
rs2622284	0.85[ASN][1000 genomes]
rs2622285	0.85[ASN][1000 genomes]
rs2622286	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622293	0.82[ASN][1000 genomes]
rs2622294	0.81[ASN][1000 genomes]
rs2622297	0.81[ASN][1000 genomes]
rs2622298	0.82[ASN][1000 genomes]
rs2622299	0.82[ASN][1000 genomes]
rs2622304	0.82[ASN][1000 genomes]
rs2622307	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2753066	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2758224	0.85[ASN][1000 genomes]
rs2758225	0.85[ASN][1000 genomes]
rs2758226	0.83[ASN][1000 genomes]
rs2758228	0.82[ASN][1000 genomes]
rs2758229	0.81[ASN][1000 genomes]
rs2758230	0.81[ASN][1000 genomes]
rs2758231	0.82[ASN][1000 genomes]
rs2758232	0.85[ASN][1000 genomes]
rs2758233	0.80[ASN][1000 genomes]
rs2758234	0.82[ASN][1000 genomes]
rs2758236	0.82[ASN][1000 genomes]
rs2758237	0.82[ASN][1000 genomes]
rs2758238	0.82[ASN][1000 genomes]
rs2758247	0.85[ASN][1000 genomes]
rs2758248	0.82[ASN][1000 genomes]
rs2758250	0.85[ASN][1000 genomes]
rs2758259	0.85[ASN][1000 genomes]
rs2800017	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800018	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800023	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800027	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800044	0.82[ASN][1000 genomes]
rs2800045	0.82[ASN][1000 genomes]
rs2800047	0.82[ASN][1000 genomes]
rs2800048	0.82[ASN][1000 genomes]
rs2800049	0.85[ASN][1000 genomes]
rs2800050	0.85[ASN][1000 genomes]
rs2800051	0.85[ASN][1000 genomes]
rs2800052	0.85[ASN][1000 genomes]
rs2984458	0.82[ASN][1000 genomes]
rs4299811	0.87[ASN][1000 genomes]
rs4358600	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445042	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4482958	0.87[ASN][1000 genomes]
rs4557499	0.87[ASN][1000 genomes]
rs4710254	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4710255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4710430	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4710431	0.90[ASN][1000 genomes]
rs6454235	0.85[ASN][1000 genomes]
rs6454236	0.85[ASN][1000 genomes]
rs6454244	0.82[ASN][1000 genomes]
rs6919709	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6924479	0.91[ASN][1000 genomes]
rs6929702	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6938965	0.87[ASN][1000 genomes]
rs6939324	0.85[ASN][1000 genomes]
rs6939983	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6942342	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs733912	0.82[ASN][1000 genomes]
rs7738916	0.82[ASN][1000 genomes]
rs7742595	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745873	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7763834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773557	0.82[ASN][1000 genomes]
rs9294196	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294197	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294198	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294202	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9294206	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9294215	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294229	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9294234	0.87[ASN][1000 genomes]
rs9341835	0.81[ASN][1000 genomes]
rs9341841	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9341893	0.83[ASN][1000 genomes]
rs9344090	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9344129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344137	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344168	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9344188	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9350913	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9350929	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9353004	0.86[ASN][1000 genomes]
rs9353015	0.87[ASN][1000 genomes]
rs9353016	0.87[ASN][1000 genomes]
rs9353017	0.87[ASN][1000 genomes]
rs9353023	0.85[ASN][1000 genomes]
rs9359467	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9361762	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9361767	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9361779	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9361816	0.85[ASN][1000 genomes]
rs9361827	0.85[ASN][1000 genomes]
rs9361829	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9361838	0.87[ASN][1000 genomes]
rs9361844	0.87[ASN][1000 genomes]
rs9443919	0.83[ASN][1000 genomes]
rs9443921	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9443931	0.87[ASN][1000 genomes]
rs9449233	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9449291	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9449297	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9449312	0.96[ASN][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
rs9352960	LGSN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64146600-64158000	Weak transcription	Hela-S3	cervix
2	chr6:64149400-64152400	Active TSS	A549	lung
3	chr6:64149600-64152400	Enhancers	HepG2	liver
4	chr6:64150000-64150600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:64150000-64150600	Enhancers	Placenta	Placenta
6	chr6:64150000-64150800	Enhancers	Stomach Mucosa	stomach
7	chr6:64150400-64150800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:64150400-64151400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:64150400-64151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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