Variant report

Variant	rs12478653
Chromosome Location	chr2:86535394-86535395
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86535378..86537907-chr2:86539539..86542949,4	MCF-7	breast:
2	chr2:86530903..86533565-chr2:86534462..86536704,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10186289	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs10189492	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10200186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200619	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10201457	0.81[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs10520415	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11127026	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11674249	0.81[ASN][1000 genomes]
rs11675942	0.82[JPT][hapmap]
rs11681689	0.82[JPT][hapmap]
rs11685863	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11691726	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11691807	0.82[JPT][hapmap]
rs12052607	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12466728	0.82[JPT][hapmap]
rs12469233	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12472390	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12472676	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476706	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12476826	0.82[JPT][hapmap]
rs12478575	0.96[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]
rs12620833	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12622200	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12714179	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714180	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988844	0.82[JPT][hapmap]
rs12999029	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13015186	0.88[CEU][hapmap];0.85[AMR][1000 genomes]
rs13017143	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[AMR][1000 genomes]
rs13017338	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018801	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13020869	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023154	0.88[CEU][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13024964	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13421310	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17438687	0.82[JPT][hapmap]
rs17737955	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17738096	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863051	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs1863052	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1863059	0.82[JPT][hapmap]
rs1863063	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs2278105	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34048420	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34069316	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35160687	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35281683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35370705	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35494267	0.80[ASN][1000 genomes]
rs35762338	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392258	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4832031	0.82[JPT][hapmap]
rs4832033	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4832261	0.82[JPT][hapmap]
rs4832262	0.82[JPT][hapmap]
rs4832269	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4832270	0.82[JPT][hapmap]
rs6547668	0.82[JPT][hapmap]
rs6547673	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6713456	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714362	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6725234	0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6738585	0.80[ASN][1000 genomes]
rs67407963	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6745235	0.82[JPT][hapmap]
rs6746198	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs67903513	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560886	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7563887	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7571424	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7593440	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9677502	0.82[JPT][hapmap]

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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12478653	IMMT	cis	Whole Blood	GTEx
rs12478653	ZNF384	trans	parietal	SCAN
rs12478653	MRPL35	cis	cerebellum	SCAN
rs12478653	MRPL35	cis	parietal	SCAN
rs12478653	IMMT	cis	cerebellum	SCAN
rs12478653	REEP1	cis	multi-tissue	Pritchard
rs12478653	REEP1	cis	parietal	SCAN
rs12478653	VAMP5	cis	parietal	SCAN
rs12478653	REEP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86525800-86540800	Weak transcription	Aorta	Aorta
2	chr2:86529400-86535600	Weak transcription	Psoas Muscle	Psoas
3	chr2:86529400-86535600	Weak transcription	Right Ventricle	heart
4	chr2:86529400-86539200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:86529600-86535600	Weak transcription	Right Atrium	heart
6	chr2:86529800-86537200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:86530000-86537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:86530200-86535800	Weak transcription	HSMMtube	muscle
9	chr2:86532800-86535600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:86533000-86538600	Weak transcription	Fetal Brain Female	brain
11	chr2:86533000-86542800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:86533200-86563000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:86533400-86535800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:86533600-86538000	Weak transcription	Fetal Lung	lung
15	chr2:86534600-86536600	Enhancers	Left Ventricle	heart
16	chr2:86534600-86536600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:86534600-86538200	Enhancers	Fetal Heart	heart
18	chr2:86534800-86537200	Enhancers	Fetal Muscle Leg	muscle
19	chr2:86535000-86535400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:86535200-86537000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:86535200-86537400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:86535200-86539600	Enhancers	Rectal Smooth Muscle	rectum

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