Variant report

Variant	rs4244600
Chromosome Location	chr17:19569026-19569027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1004490	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1004491	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1034897	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601634	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12604069	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12940877	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12945345	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16960251	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2072332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120271	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28672254	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2891951	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35364675	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752046	0.81[EUR][1000 genomes]
rs3786038	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4621031	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4646793	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646800	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924788	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924791	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925002	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4925026	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925037	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925040	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4925041	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56262978	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58835440	0.81[EUR][1000 genomes]
rs58970893	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61631401	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67870359	0.81[EUR][1000 genomes]
rs68066777	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7216938	0.80[EUR][1000 genomes]
rs73981559	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7502080	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962801	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs968012	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9902636	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909886	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9914765	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4244600	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs4244600	ALDH3A2	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
6	chr17:19555200-19569800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:19555400-19570000	Strong transcription	Fetal Muscle Leg	muscle
9	chr17:19555600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
11	chr17:19556200-19569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr17:19556600-19569800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:19557200-19569800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:19558200-19569400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:19558200-19569600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:19558200-19569800	Strong transcription	Fetal Intestine Large	intestine
17	chr17:19558400-19571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:19558600-19569800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr17:19559200-19571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:19559200-19574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr17:19559400-19575000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:19559400-19575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr17:19559600-19570800	Strong transcription	Brain Anterior Caudate	brain
25	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:19561200-19570600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:19561400-19569800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr17:19563400-19569800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr17:19563400-19569800	Strong transcription	Fetal Brain Female	brain
31	chr17:19563400-19569800	Strong transcription	Fetal Lung	lung
32	chr17:19563600-19569200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:19563600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr17:19564000-19569400	Strong transcription	HSMMtube	muscle
35	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
36	chr17:19564200-19569800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr17:19564200-19569800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr17:19564400-19571000	Strong transcription	A549	lung
39	chr17:19564600-19569200	Genic enhancers	HepG2	liver
40	chr17:19564600-19569600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr17:19564600-19569800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:19564600-19571200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:19564800-19569600	Strong transcription	Rectal Smooth Muscle	rectum
44	chr17:19564800-19569800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr17:19564800-19569800	Strong transcription	Ovary	ovary
46	chr17:19564800-19570000	Strong transcription	Colonic Mucosa	Colon
47	chr17:19564800-19574600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:19565000-19569800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:19565200-19569400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr17:19565200-19569800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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