Variant report

Variant	rs12790378
Chromosome Location	chr11:34439880-34439881
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34438694..34440989-chr11:34441788..34444701,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001179	0.88[CHD][hapmap];0.82[MEX][hapmap]
rs1008491	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10836215	0.92[EUR][1000 genomes]
rs10836223	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10836229	0.83[ASN][1000 genomes]
rs10836230	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10836234	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11032654	1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11032661	1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032667	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032670	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032671	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032682	0.92[ASN][1000 genomes]
rs11032695	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11032726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11604331	0.88[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12361866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790004	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793666	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12797274	0.88[CHD][hapmap]
rs12804506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12806377	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807961	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12808450	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1408041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17269903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17352313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2231825	0.88[CHD][hapmap]
rs2231828	0.88[CHD][hapmap]
rs2420386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34329347	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34533645	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35725681	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs494024	0.88[CHD][hapmap];0.86[GIH][hapmap]
rs499406	0.88[CHD][hapmap];0.85[GIH][hapmap]
rs511895	0.88[CHD][hapmap];0.86[GIH][hapmap]
rs524167	0.88[CHD][hapmap];0.86[GIH][hapmap]
rs533425	0.88[CHD][hapmap];0.86[GIH][hapmap]
rs55892947	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59090359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66679411	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737254	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs873466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910089	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv983151	chr11:34401342-34444667	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12790378	CAT	cis	multi-tissue	Pritchard
rs12790378	TEX264	trans	parietal	SCAN
rs12790378	CAT	cis	Whole Blood	GTEx
rs12790378	DEPDC7	cis	parietal	SCAN
rs12790378	CAT	cis	lymphoblastoid	seeQTL
rs12790378	CAT	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34436200-34440200	Enhancers	Liver	Liver
2	chr11:34437200-34441200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:34437200-34446200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:34437600-34440400	Enhancers	Adipose Nuclei	Adipose
5	chr11:34438200-34440200	Enhancers	Hela-S3	cervix
6	chr11:34438200-34440400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:34438200-34440400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:34438200-34448600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr11:34438600-34443800	Weak transcription	Primary B cells from cord blood	blood
10	chr11:34439000-34443600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr11:34439400-34440200	Enhancers	Fetal Kidney	kidney
12	chr11:34439400-34440400	Enhancers	HepG2	liver
13	chr11:34439600-34440200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:34439600-34440200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:34439600-34440400	Enhancers	Primary hematopoietic stem cells	blood
16	chr11:34439800-34440000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:34439800-34440000	Enhancers	Lung	lung
18	chr11:34439800-34440200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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