Variant report

Variant	rs4369447
Chromosome Location	chr12:29394585-29394586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10492383	1.00[CEU][hapmap]
rs11608616	1.00[CEU][hapmap]
rs11609540	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11610197	1.00[CEU][hapmap]
rs11610910	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11611687	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11612172	0.91[EUR][1000 genomes]
rs11613628	0.85[EUR][1000 genomes]
rs11614129	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11614901	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11615636	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12314737	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs12809077	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811723	1.00[CEU][hapmap]
rs12813996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12814180	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12814930	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12815222	1.00[CEU][hapmap]
rs12816511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817163	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817825	0.91[EUR][1000 genomes]
rs12817985	0.91[EUR][1000 genomes]
rs12819896	1.00[CEU][hapmap]
rs12821498	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12822770	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823372	0.83[EUR][1000 genomes]
rs12823422	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823485	0.85[EUR][1000 genomes]
rs12823903	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12826064	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12829666	1.00[CEU][hapmap]
rs12830274	0.91[EUR][1000 genomes]
rs12830493	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12830678	1.00[CEU][hapmap]
rs12830906	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12831730	1.00[CEU][hapmap]
rs12832038	1.00[CEU][hapmap]
rs12832263	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16934061	0.99[EUR][1000 genomes]
rs1988943	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2350312	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882377	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34162895	0.80[AMR][1000 genomes]
rs35636563	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36040692	0.80[EUR][1000 genomes]
rs36126531	0.80[AMR][1000 genomes]
rs3764952	1.00[CEU][hapmap]
rs67280216	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67324531	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134744	0.84[EUR][1000 genomes]
rs7299158	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299635	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299663	0.97[EUR][1000 genomes]
rs7308372	1.00[CEU][hapmap]
rs7314594	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7961336	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7964254	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979654	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3431050	chr12:29394152-29394604	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4369447	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4369447	RP11-996F15.2	cis	Artery Tibial	GTEx
rs4369447	RP11-996F15.2	cis	Thyroid	GTEx
rs4369447	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs4369447	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs4369447	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs4369447	RP11-996F15.2	cis	lung	GTEx
rs4369447	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs4369447	RP11-996F15.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29379600-29394600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:29381800-29394600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:29381800-29394800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:29388600-29394800	Weak transcription	NHEK	skin
5	chr12:29388800-29394600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:29390200-29394800	Enhancers	HUVEC	blood vessel
7	chr12:29391600-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:29391800-29394600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:29391800-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:29392200-29394600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:29392400-29394600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:29392400-29394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:29392400-29394600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:29392400-29394600	Weak transcription	NH-A	brain
15	chr12:29392400-29395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:29392400-29395400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:29392800-29396000	Enhancers	Placenta	Placenta
18	chr12:29393200-29394600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr12:29393200-29394600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:29393200-29395000	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:29393200-29396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:29393200-29397000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:29393400-29394600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:29393400-29394600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:29393400-29394600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:29393400-29395400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:29393400-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:29393400-29396000	Enhancers	Duodenum Mucosa	Duodenum
29	chr12:29393400-29396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:29393600-29394600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:29393600-29394600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:29393600-29394600	Weak transcription	Fetal Intestine Large	intestine
33	chr12:29393600-29394600	Weak transcription	Fetal Thymus	thymus
34	chr12:29393600-29394600	Weak transcription	Lung	lung
35	chr12:29393600-29394600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:29394000-29395800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:29394000-29395800	Enhancers	Stomach Smooth Muscle	stomach
38	chr12:29394000-29396200	Enhancers	Colonic Mucosa	Colon
39	chr12:29394000-29396200	Enhancers	NHDF-Ad	bronchial
40	chr12:29394200-29394600	Enhancers	Adipose Nuclei	Adipose
41	chr12:29394200-29395400	Enhancers	Primary B cells from cord blood	blood
42	chr12:29394200-29396000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr12:29394200-29396200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr12:29394200-29396200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr12:29394200-29396800	Enhancers	Stomach Mucosa	stomach
46	chr12:29394400-29394600	Enhancers	Osteobl	bone
47	chr12:29394400-29394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:29394400-29395000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr12:29394400-29395800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:29394400-29395800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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