Variant report

Variant	rs4780053
Chromosome Location	chr15:33163454-33163455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12591087	0.87[CHB][hapmap]
rs12594394	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16960230	0.83[YRI][hapmap]
rs17228887	0.87[CHB][hapmap]
rs4780055	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4780056	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62001315	0.93[EUR][1000 genomes]
rs62001318	0.85[EUR][1000 genomes]
rs62001319	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72717700	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8026174	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8027463	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs8032518	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv832962	chr15:33111517-33239736	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv903980	chr15:33149087-33264201	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4780053	HOXA3	trans	cerebellum	SCAN
rs4780053	NDNL2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33131800-33164800	Weak transcription	Pancreas	Pancrea
2	chr15:33138800-33190600	Weak transcription	Thymus	Thymus
3	chr15:33139600-33190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:33142600-33168200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:33147000-33191400	Weak transcription	Lung	lung
6	chr15:33149000-33202000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:33149600-33169600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:33153800-33173200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:33154400-33164000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:33154400-33164600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:33154400-33173800	Weak transcription	Placenta	Placenta
12	chr15:33154400-33192800	Weak transcription	Colonic Mucosa	Colon
13	chr15:33154400-33216800	Weak transcription	Fetal Thymus	thymus
14	chr15:33155000-33208200	Weak transcription	Fetal Kidney	kidney
15	chr15:33155200-33164400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:33155200-33164800	Weak transcription	Ovary	ovary
17	chr15:33156600-33164000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:33157200-33163800	Weak transcription	Brain Angular Gyrus	brain
19	chr15:33157400-33163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:33159400-33164200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:33159400-33164400	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:33159400-33164400	Weak transcription	Fetal Lung	lung
23	chr15:33159400-33166600	Weak transcription	Stomach Mucosa	stomach
24	chr15:33159600-33165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:33159800-33164400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:33159800-33165200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:33159800-33169400	Weak transcription	HUVEC	blood vessel
28	chr15:33160000-33164800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:33160000-33201800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:33160400-33164600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:33160400-33166600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr15:33160800-33164000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:33161200-33165600	Enhancers	Stomach Smooth Muscle	stomach
34	chr15:33161200-33166200	Enhancers	NHDF-Ad	bronchial
35	chr15:33161600-33166000	Enhancers	NHLF	lung
36	chr15:33162000-33164000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:33162000-33168200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:33162000-33178400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:33162200-33176400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:33162200-33202400	Weak transcription	Gastric	stomach
41	chr15:33162400-33164400	Weak transcription	Adipose Nuclei	Adipose
42	chr15:33162400-33166800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr15:33162600-33166200	Enhancers	HSMMtube	muscle
44	chr15:33162800-33165000	Weak transcription	A549	lung
45	chr15:33163000-33164200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:33163200-33166200	Genic enhancers	HSMM	muscle
47	chr15:33163400-33163800	Weak transcription	Fetal Stomach	stomach
48	chr15:33163400-33165000	Genic enhancers	Osteobl	bone
49	chr15:33163400-33165400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:33163400-33169600	Weak transcription	NH-A	brain

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