Variant report

Variant	rs494632
Chromosome Location	chr12:121189116-121189117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121186636..121188144-chr12:121188175..121190452,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10774572	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10849791	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10849807	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs11065264	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11065282	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11065283	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11065284	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11065292	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11065293	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11065300	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs11065311	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs11065324	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs1151849	0.86[JPT][hapmap]
rs1151862	0.86[JPT][hapmap]
rs11608262	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11611087	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1177585	0.86[JPT][hapmap]
rs12579868	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12580949	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs12809299	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822123	0.96[CEU][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap]
rs12824150	0.86[CEU][hapmap]
rs13746	0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1467283	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1542859	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs1696357	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2047568	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2062507	0.85[CEU][hapmap]
rs2393717	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs2893876	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3213566	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs3213570	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3213572	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34076777	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35706672	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3809313	0.84[CEU][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs3842985	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3861797	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3883901	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3897746	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs3901854	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4454799	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs471688	0.86[JPT][hapmap]
rs4766979	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4767935	0.85[CEU][hapmap]
rs4767937	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508595	0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs525425	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs531782	0.86[JPT][hapmap]
rs534415	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs580240	0.86[EUR][1000 genomes]
rs58291418	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs608394	0.87[EUR][1000 genomes]
rs610694	0.86[JPT][hapmap]
rs618482	0.84[EUR][1000 genomes]
rs624216	0.90[JPT][hapmap]
rs625228	0.86[JPT][hapmap]
rs661647	0.85[JPT][hapmap]
rs7137504	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7305849	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs869781	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs909053	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9431	0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs989986	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs989987	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs494632	SPPL3	cis	Nerve Tibial	GTEx
rs494632	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs494632	ACADS	cis	Thyroid	GTEx
rs494632	SPPL3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121168600-121196400	Weak transcription	Fetal Brain Female	brain
2	chr12:121177800-121197800	Weak transcription	Gastric	stomach
3	chr12:121178000-121194400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:121179800-121197400	Weak transcription	Spleen	Spleen
5	chr12:121180200-121197400	Weak transcription	Pancreas	Pancrea
6	chr12:121183200-121197600	Weak transcription	Esophagus	oesophagus
7	chr12:121186200-121189200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:121186400-121198400	Weak transcription	Right Ventricle	heart
9	chr12:121186600-121192400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:121187200-121189400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:121187400-121189400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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