Variant report

Variant	rs12529733
Chromosome Location	chr6:109654132-109654133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109649495..109651298-chr6:109651628..109654623,3	K562	blood:
2	chr6:109652681..109655937-chr6:109701274..109703936,3	MCF-7	breast:
3	chr6:109652928..109655072-chr6:109655937..109657890,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10457192	0.84[CEU][hapmap]
rs10457194	0.83[CEU][hapmap]
rs1046943	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1074765	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1074766	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10872033	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11153183	0.83[CEU][hapmap]
rs11251	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs11754455	0.84[CEU][hapmap]
rs12197180	0.84[CEU][hapmap]
rs12198938	0.84[CEU][hapmap]
rs12199154	0.83[CEU][hapmap]
rs12212476	0.84[CEU][hapmap]
rs12214147	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13219952	0.88[EUR][1000 genomes]
rs13220915	0.84[CEU][hapmap]
rs1406899	0.84[CEU][hapmap]
rs1476387	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1521907	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17070591	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1853330	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1885690	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1885691	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2024850	0.83[CEU][hapmap]
rs2024853	0.84[CEU][hapmap]
rs2211288	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236084	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2277113	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2277114	0.83[CEU][hapmap]
rs2884037	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35146243	0.81[EUR][1000 genomes]
rs3734652	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs3757230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757231	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757235	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778474	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs3778478	0.81[EUR][1000 genomes]
rs3799842	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs3818933	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4636056	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945831	0.88[EUR][1000 genomes]
rs4946967	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs4946970	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946976	0.83[EUR][1000 genomes]
rs58644322	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59597139	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6914216	0.87[EUR][1000 genomes]
rs6920372	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920962	0.86[CHB][hapmap]
rs6939548	0.81[EUR][1000 genomes]
rs6939953	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs699700	0.90[EUR][1000 genomes]
rs730089	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736830	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs746794	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7748669	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7751582	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7754650	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7755941	0.83[CEU][hapmap]
rs7768973	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773950	0.84[CEU][hapmap]
rs8465	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910730	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9320286	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9372213	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9386799	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9398202	0.85[CEU][hapmap]
rs9480930	0.84[EUR][1000 genomes]
rs9480947	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9480949	0.86[EUR][1000 genomes]
rs9480956	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9480958	0.88[EUR][1000 genomes]
rs9487064	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487066	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487069	0.90[EUR][1000 genomes]
rs9487070	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487076	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487084	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487085	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487103	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974034	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9791241	0.96[CEU][hapmap];0.81[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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12529733	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12529733	MICAL1	cis	Artery Tibial	GTEx
rs12529733	SMPD2	cis	Esophagus Mucosa	GTEx
rs12529733	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109644800-109657400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
4	chr6:109651600-109654600	Enhancers	Stomach Mucosa	stomach
5	chr6:109653000-109655000	Enhancers	Fetal Intestine Large	intestine
6	chr6:109653000-109655000	Enhancers	Fetal Intestine Small	intestine
7	chr6:109653000-109655000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr6:109653400-109654400	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:109653400-109654400	Active TSS	Rectal Smooth Muscle	rectum
10	chr6:109653400-109654400	Enhancers	Right Ventricle	heart
11	chr6:109653400-109658800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr6:109653600-109654200	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:109653600-109654200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:109653600-109654200	Enhancers	Spleen	Spleen
15	chr6:109653600-109654400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:109653600-109654400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:109653600-109654600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:109653600-109654600	Enhancers	HepG2	liver
19	chr6:109653800-109654200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr6:109653800-109654200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:109653800-109654200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:109653800-109654400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr6:109653800-109654400	Enhancers	Esophagus	oesophagus
24	chr6:109653800-109654400	Enhancers	Gastric	stomach
25	chr6:109653800-109654400	Enhancers	Lung	lung
26	chr6:109653800-109654400	Enhancers	Hela-S3	cervix
27	chr6:109653800-109656400	Weak transcription	Colonic Mucosa	Colon
28	chr6:109654000-109654400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:109654000-109654400	Enhancers	Fetal Muscle Leg	muscle
30	chr6:109654000-109654400	Enhancers	Placenta	Placenta
31	chr6:109654000-109654400	Enhancers	K562	blood
32	chr6:109654000-109657400	Weak transcription	Pancreas	Pancrea
33	chr6:109654000-109657600	Weak transcription	Adipose Nuclei	Adipose
34	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine

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