Variant report

Variant	rs2288806
Chromosome Location	chr5:146775475-146775476
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10052013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10059782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11738683	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11738709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12655364	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1432836	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17106658	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864962	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288803	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2288804	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288808	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2304045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213856	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34784063	0.99[ASN][1000 genomes]
rs3805536	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs3816013	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs4235731	0.84[GIH][hapmap]
rs4705168	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705169	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60953985	0.93[ASN][1000 genomes]
rs6887761	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6892646	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7725904	1.00[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]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2288806	NR3C1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146762800-146775600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:146762800-146775600	Weak transcription	Placenta	Placenta
3	chr5:146762800-146775600	Weak transcription	Left Ventricle	heart
4	chr5:146762800-146775600	Weak transcription	Right Ventricle	heart
5	chr5:146762800-146783400	Weak transcription	Pancreas	Pancrea
6	chr5:146762800-146784200	Weak transcription	Colonic Mucosa	Colon
7	chr5:146764400-146777400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:146766200-146775800	Weak transcription	Lung	lung
9	chr5:146767400-146782200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
11	chr5:146768000-146784000	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:146768600-146783400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:146769000-146783000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr5:146770200-146784800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:146770400-146775600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:146770400-146777200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr5:146770400-146779000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:146770400-146783000	Strong transcription	Fetal Muscle Leg	muscle
24	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
25	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:146770600-146781600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr5:146770600-146782000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:146770600-146782800	Weak transcription	Fetal Heart	heart
29	chr5:146770600-146783200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:146770600-146783400	Strong transcription	Fetal Stomach	stomach
31	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:146770800-146777000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:146771000-146775800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:146771000-146781600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:146771200-146775800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:146771600-146786600	Weak transcription	Gastric	stomach
38	chr5:146771800-146777200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:146771800-146780800	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr5:146771800-146782000	Strong transcription	NH-A	brain
41	chr5:146772000-146781400	Strong transcription	Colon Smooth Muscle	Colon
42	chr5:146772000-146782600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:146772200-146775600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:146772400-146783800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:146772600-146775600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:146772600-146778600	Strong transcription	Aorta	Aorta
47	chr5:146772600-146778800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:146772600-146778800	Strong transcription	Rectal Smooth Muscle	rectum
49	chr5:146772600-146779800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:146772600-146781400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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