Variant report

Variant	rs9829949
Chromosome Location	chr3:134126150-134126151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10222468	0.92[EUR][1000 genomes]
rs10433422	0.88[EUR][1000 genomes]
rs2133306	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs3846051	0.83[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3913264	0.84[EUR][1000 genomes]
rs4974503	0.88[EUR][1000 genomes]
rs4998531	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771287	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6783899	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7431009	0.97[ASN][1000 genomes]
rs7624209	0.83[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs9289470	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9842071	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9849457	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs9853685	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9866933	0.88[EUR][1000 genomes]
rs9879839	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9829949	CDH1	trans	lymphoblastoid	seeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134124400-134126600	Enhancers	Fetal Brain Male	brain
2	chr3:134124600-134126200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:134124600-134126200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:134124600-134126200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:134125000-134126200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr3:134125000-134126200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:134125000-134126200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:134125000-134126200	Active TSS	Brain Anterior Caudate	brain
9	chr3:134125000-134126200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
10	chr3:134125000-134126200	Bivalent Enhancer	Fetal Thymus	thymus
11	chr3:134125000-134126400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:134125000-134126600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr3:134125000-134126600	Enhancers	Fetal Heart	heart
14	chr3:134125200-134126200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:134125200-134126200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:134125200-134126200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:134125200-134126200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:134125200-134126200	Active TSS	Right Atrium	heart
19	chr3:134125200-134126400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:134125200-134126600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:134125400-134126400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:134125800-134126200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:134125800-134126200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
24	chr3:134125800-134126200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
25	chr3:134125800-134126200	Enhancers	NHLF	lung
26	chr3:134125800-134126200	Flanking Active TSS	Osteobl	bone
27	chr3:134125800-134126400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
28	chr3:134125800-134126400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:134125800-134126400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr3:134125800-134126600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr3:134126000-134126200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:134126000-134126200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:134126000-134126200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:134126000-134126200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:134126000-134126200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
36	chr3:134126000-134126200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:134126000-134126200	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr3:134126000-134126200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:134126000-134126200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
40	chr3:134126000-134126200	Enhancers	Esophagus	oesophagus
41	chr3:134126000-134126200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr3:134126000-134126200	Flanking Active TSS	Fetal Brain Female	brain
43	chr3:134126000-134126200	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr3:134126000-134126200	Enhancers	Ovary	ovary
45	chr3:134126000-134126200	Enhancers	Rectal Smooth Muscle	rectum
46	chr3:134126000-134126200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:134126000-134126200	Bivalent Enhancer	Stomach Mucosa	stomach
48	chr3:134126000-134126400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:134126000-134126400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:134126000-134126400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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