Variant report

Variant	rs9261470
Chromosome Location	chr6:30104808-30104809
allele	A/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	POLR2A	chr6:30104770-30105003	MCF-7	breast:	n/a	n/a
2	RUNX3	chr6:30104208-30104850	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:30104642-30104821	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30028084..30030840-chr6:30103303..30105686,3	MCF-7	breast:
2	chr6:30097580..30101195-chr6:30103058..30105479,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM15-1	chr6:30104510-30104975	NONHSAT108605

Variant related genes	Relation type
ENSG00000252228	TF binding region
ENSG00000204623	Chromatin interaction
ENSG00000252228	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1042338	0.83[EUR][1000 genomes]
rs1076229	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947053	0.88[ASN][1000 genomes]
rs13194768	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1419671	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1419672	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1419673	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1541324	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1573297	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573298	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1573299	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17194607	0.80[EUR][1000 genomes]
rs2239530	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2284163	0.88[ASN][1000 genomes]
rs2285795	0.85[EUR][1000 genomes]
rs2285796	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2508030	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2508031	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2517653	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517655	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28400887	0.81[ASN][1000 genomes]
rs2857433	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2857435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857436	0.94[ASN][1000 genomes]
rs2857438	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857439	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857440	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857458	0.94[ASN][1000 genomes]
rs3778622	0.81[EUR][1000 genomes]
rs3815079	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815080	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815082	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3815084	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3815085	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3815086	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888580	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4392759	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711211	0.81[EUR][1000 genomes]
rs4713293	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959011	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4959012	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959041	0.88[ASN][1000 genomes]
rs4959044	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757259	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757261	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757262	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757263	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757264	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7843	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9261424	0.88[ASN][1000 genomes]
rs9261431	0.88[ASN][1000 genomes]
rs9261433	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261438	0.88[ASN][1000 genomes]
rs9261439	0.88[ASN][1000 genomes]
rs9261440	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261442	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261443	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261444	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261445	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261446	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261448	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261449	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261450	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261451	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261453	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261454	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261455	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261456	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261457	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261458	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261459	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261461	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261462	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261467	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261471	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261472	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261473	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261480	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261481	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261482	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261483	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261484	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261485	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261486	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261488	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261489	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261490	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261491	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261492	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261493	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261495	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261496	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261497	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261498	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261499	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261500	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261501	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261502	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261503	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261504	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261505	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261507	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261508	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261509	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261511	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261512	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261513	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261514	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261516	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261517	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261518	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261519	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261521	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261522	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261523	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261524	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261525	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261526	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261527	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261528	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261529	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261530	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261531	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261532	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261533	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261535	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs929156	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs957765	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9261470	HIST1H2BN	cis	parietal	SCAN
rs9261470	HIST1H2AM	cis	parietal	SCAN
rs9261470	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9261470	ZKSCAN3	cis	cerebellum	SCAN
rs9261470	BTN2A1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30101800-30105000	Enhancers	Fetal Intestine Large	intestine
2	chr6:30103800-30105000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:30103800-30105000	Enhancers	Small Intestine	intestine
4	chr6:30103800-30105400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:30103800-30105400	Enhancers	HepG2	liver
6	chr6:30103800-30107400	Active TSS	Placenta	Placenta
7	chr6:30104200-30106400	Weak transcription	Stomach Mucosa	stomach
8	chr6:30104600-30105000	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr6:30104600-30105000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
10	chr6:30104600-30105200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:30104600-30105400	Active TSS	Colonic Mucosa	Colon
12	chr6:30104800-30105200	Enhancers	Fetal Intestine Small	intestine

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