Variant report

Variant	rs2732529
Chromosome Location	chr11:35036759-35036760
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1035731	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1425804	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1477562	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1477563	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1559756	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2433161	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2433162	0.90[EUR][1000 genomes]
rs2467603	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2469910	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2553787	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2553788	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2553789	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2553790	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2553791	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2553792	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2553793	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2553794	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2553795	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2553797	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2553800	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553801	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553802	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2553803	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2553805	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2553806	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2732520	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732521	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732522	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732524	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2732526	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2732527	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2732528	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2785153	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2785154	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2785155	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2785156	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2785157	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2785159	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2785160	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2785161	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2785162	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2785163	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2785166	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2785167	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2785168	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2785169	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs471450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs496623	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs497476	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs532282	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs536864	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs603820	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs622235	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs663993	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs666197	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs678137	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7479679	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv430371	chr11:34975067-35111292	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1826391	chr11:35000983-35098193	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv897215	chr11:35009233-35048359	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv540999	chr11:35021936-35185471	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv2758263	chr11:35029933-35226784	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2759818	chr11:35029933-35238578	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2732529	PDHX	cis	multi-tissue	Pritchard
rs2732529	EHF	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35028400-35039600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:35028600-35051600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:35030000-35037400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:35032200-35037600	Weak transcription	Fetal Intestine Large	intestine
5	chr11:35032800-35037800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:35033000-35039200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:35033000-35039200	Weak transcription	HepG2	liver
8	chr11:35033000-35039400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:35033200-35037000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:35033200-35043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:35033600-35051200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:35034800-35037200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:35035400-35037200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr11:35035400-35039400	Weak transcription	Pancreas	Pancrea
15	chr11:35035600-35039200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:35035800-35037600	Weak transcription	Stomach Mucosa	stomach
17	chr11:35036000-35037200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:35036000-35037800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:35036000-35038000	Enhancers	NHDF-Ad	bronchial
20	chr11:35036000-35038400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:35036000-35038600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:35036000-35039000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:35036200-35037200	Weak transcription	Primary T cells from cord blood	blood
24	chr11:35036200-35037200	Weak transcription	Fetal Lung	lung
25	chr11:35036200-35039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:35036200-35041800	Weak transcription	Spleen	Spleen
27	chr11:35036200-35043000	Weak transcription	HSMMtube	muscle
28	chr11:35036400-35039000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:35036600-35037000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:35036600-35037000	Weak transcription	Fetal Stomach	stomach
31	chr11:35036600-35037200	Enhancers	Fetal Muscle Leg	muscle
32	chr11:35036600-35039200	Weak transcription	Osteobl	bone

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