Variant report

Variant	rs12212476
Chromosome Location	chr6:109822605-109822606
allele	C/T
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	CEBPB	chr6:109822572-109822735	Hela-S3	cervix:	n/a	chr6:109822622-109822635 chr6:109822623-109822634
2	CEBPB	chr6:109822499-109822870	A549	lung:	n/a	chr6:109822622-109822635 chr6:109822623-109822634
3	CEBPB	chr6:109822475-109822731	HepG2	liver:	n/a	chr6:109822622-109822635 chr6:109822623-109822634

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109808551..109810943-chr6:109821241..109824153,2	MCF-7	breast:
2	chr6:109822082..109824887-chr6:109829770..109832005,2	K562	blood:

Variant related genes	Relation type
ENSG00000253037	TF binding region
ENSG00000223537	Chromatin interaction

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

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

rs_ID	r²[population]
rs10457192	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10457203	0.83[EUR][1000 genomes]
rs1046943	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1048203	0.86[CHB][hapmap]
rs10499053	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1074765	0.87[CEU][hapmap]
rs1074766	0.87[CEU][hapmap]
rs10782162	0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs10782163	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872034	0.95[ASN][1000 genomes]
rs11153174	0.86[CHB][hapmap]
rs11153175	0.86[CHB][hapmap]
rs11153183	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs11153188	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153213	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[YRI][hapmap]
rs11251	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs11752791	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11754340	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11754455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967108	0.86[CHB][hapmap]
rs12190920	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12190996	0.84[ASN][1000 genomes]
rs12191353	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12192268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs12192776	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192847	0.85[ASN][1000 genomes]
rs12193719	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12194061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12194157	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195904	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12197114	0.86[CHB][hapmap]
rs12197180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197838	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12197950	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198938	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205140	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12205485	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208018	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208933	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs12209691	0.85[ASN][1000 genomes]
rs12210706	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12214639	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12524639	0.86[CHB][hapmap]
rs12528781	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12528822	0.81[CHB][hapmap]
rs12529733	0.84[CEU][hapmap]
rs13191066	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13199109	0.82[EUR][1000 genomes]
rs13199135	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13201430	0.96[CEU][hapmap]
rs13201947	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13201951	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13203587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204102	0.82[ASN][1000 genomes]
rs13204500	0.82[ASN][1000 genomes]
rs1321328	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13220915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358998	0.86[CHB][hapmap]
rs1406899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476387	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs1476388	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546980	0.84[ASN][1000 genomes]
rs17070591	0.88[CEU][hapmap]
rs1923725	0.86[CHB][hapmap]
rs1960325	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1980591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1998811	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148089	0.80[ASN][1000 genomes]
rs2208209	0.86[ASN][1000 genomes]
rs2236084	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2236582	0.86[CHB][hapmap]
rs2275650	0.81[CHB][hapmap]
rs2277113	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs2277114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357124	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884037	0.88[CEU][hapmap]
rs35146243	0.83[EUR][1000 genomes]
rs36131450	0.81[ASN][1000 genomes]
rs3734652	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs3757234	0.86[CHB][hapmap]
rs3757235	0.87[CEU][hapmap]
rs3778474	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs3778477	0.85[ASN][1000 genomes]
rs3778478	0.83[EUR][1000 genomes]
rs3799842	0.83[CEU][hapmap]
rs3807005	0.85[ASN][1000 genomes]
rs3899233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4490694	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945833	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4946967	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs6568592	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68042406	0.95[ASN][1000 genomes]
rs6906216	0.97[ASN][1000 genomes]
rs6911700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6914498	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs6916579	0.94[ASN][1000 genomes]
rs6920292	0.88[ASN][1000 genomes]
rs6920372	0.88[CEU][hapmap]
rs6926096	0.97[ASN][1000 genomes]
rs6939548	0.83[EUR][1000 genomes]
rs71541003	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs729888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs730089	0.87[CEU][hapmap]
rs7341297	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs736830	0.87[CEU][hapmap]
rs749517	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752262	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs7748669	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs7754650	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs7755941	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767525	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7768973	0.87[CEU][hapmap]
rs7773095	0.86[CHB][hapmap]
rs7773950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910730	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs9480947	0.88[CEU][hapmap]
rs9480948	0.86[CHB][hapmap]
rs9480956	0.88[CEU][hapmap]
rs9480957	0.86[CHB][hapmap]
rs9487070	0.88[CEU][hapmap]
rs9487100	0.86[CHB][hapmap]
rs9487103	0.87[CEU][hapmap]
rs971434	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs974034	0.87[CEU][hapmap]
rs9791241	0.87[CEU][hapmap];0.83[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12212476	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12212476	SMPD2	cis	Whole Blood	GTEx
rs12212476	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs12212476	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12212476	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109813400-109823000	Weak transcription	HSMM	muscle
2	chr6:109815800-109837200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:109818200-109823400	Weak transcription	HSMMtube	muscle
4	chr6:109818400-109823000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:109818400-109823000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:109818400-109823200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:109819800-109824800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:109819800-109828200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:109819800-109828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:109820200-109824600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:109820200-109824800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:109820400-109824800	Weak transcription	Fetal Kidney	kidney
13	chr6:109822400-109826000	Enhancers	Placenta	Placenta

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