Variant report

Variant	rs11204407
Chromosome Location	chr17:19552719-19552720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19552130..19552727-chr9:115095115..115095701,2	Hela-S3	cervix:
2	chr17:19551943..19552775-chr4:164088000..164088627,2	Hela-S3	cervix:
3	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
4	chr17:19552711..19555521-chr17:19564350..19566731,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC47A2-1	chr17:19552686-19553248	ENSG00000264932.1

Variant related genes	Relation type
ENSG00000252349	Chromatin interaction
ENSG00000119314	Chromatin interaction
ENSG00000145414	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1004490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1004491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1034897	1.00[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]
rs12601634	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12602112	0.83[CHD][hapmap]
rs12604069	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12937179	0.82[CHD][hapmap]
rs12940877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12945345	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16960251	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1800869	0.86[CHD][hapmap]
rs2072331	0.84[CHD][hapmap]
rs2072332	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2120271	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2386144	0.86[CHD][hapmap]
rs28672254	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2891951	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35364675	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786038	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244600	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]
rs4621031	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4646793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646798	0.86[CHD][hapmap]
rs4646800	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924788	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924791	0.81[ASN][1000 genomes]
rs4925002	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925026	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925037	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925038	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925040	0.85[ASN][1000 genomes]
rs4925041	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56262978	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58970893	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61631401	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68066777	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7215	0.92[YRI][hapmap]
rs73981559	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7502080	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7503517	0.86[CHD][hapmap]
rs758427	0.81[GIH][hapmap]
rs962801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs968012	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9902636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9909886	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9914765	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[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	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv934250	chr17:19551657-19561421	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11204407	ALDH3A2	cis	multi-tissue	Pritchard
rs11204407	TOM1L2	cis	parietal	SCAN
rs11204407	ALDH3A2	cis	parietal	SCAN
rs11204407	ALDH3A2	cis	lymphoblastoid	seeQTL
rs11204407	ALDH3A2	cis	cerebellum	SCAN
rs11204407	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs11204407	MFAP4	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19550200-19555200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:19550600-19552800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:19550800-19553200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr17:19551000-19553000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr17:19551000-19553200	Active TSS	Brain Substantia Nigra	brain
6	chr17:19551000-19553200	Bivalent/Poised TSS	Thymus	Thymus
7	chr17:19551000-19553200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr17:19551000-19553400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr17:19551000-19553400	Active TSS	Ovary	ovary
10	chr17:19551000-19553800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr17:19551000-19553800	Active TSS	Right Ventricle	heart
12	chr17:19551000-19554600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr17:19551200-19552800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr17:19551200-19552800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr17:19551200-19552800	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr17:19551200-19552800	Active TSS	Brain Cingulate Gyrus	brain
17	chr17:19551200-19552800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr17:19551200-19552800	Active TSS	Gastric	stomach
19	chr17:19551200-19553000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:19551200-19553200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:19551200-19553200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr17:19551200-19553200	Active TSS	Colon Smooth Muscle	Colon
23	chr17:19551200-19553200	Active TSS	Left Ventricle	heart
24	chr17:19551200-19553600	Active TSS	Lung	lung
25	chr17:19551200-19553800	Active TSS	Brain Angular Gyrus	brain
26	chr17:19551200-19554000	Active TSS	Aorta	Aorta
27	chr17:19551200-19554200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr17:19551200-19554600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:19551200-19554800	Active TSS	Esophagus	oesophagus
30	chr17:19551200-19554800	Active TSS	Right Atrium	heart
31	chr17:19551400-19552800	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr17:19551400-19552800	Bivalent/Poised TSS	HepG2	liver
33	chr17:19551400-19553000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr17:19551400-19553000	Active TSS	Fetal Intestine Small	intestine
35	chr17:19551400-19553000	Active TSS	Fetal Lung	lung
36	chr17:19551400-19553000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr17:19551400-19553200	Active TSS	Stomach Mucosa	stomach
38	chr17:19551400-19553400	Active TSS	Psoas Muscle	Psoas
39	chr17:19551400-19553400	Active TSS	Rectal Smooth Muscle	rectum
40	chr17:19551400-19553400	Active TSS	NHDF-Ad	bronchial
41	chr17:19551400-19553600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr17:19551400-19553600	Active TSS	Fetal Intestine Large	intestine
43	chr17:19551400-19553600	Active TSS	Fetal Kidney	kidney
44	chr17:19551400-19553800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr17:19551400-19553800	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr17:19551400-19553800	Active TSS	Fetal Brain Female	brain
47	chr17:19551400-19554000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:19551400-19554400	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr17:19551400-19554600	Active TSS	Brain Anterior Caudate	brain
50	chr17:19551600-19552800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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