Variant report

Variant	rs1800869
Chromosome Location	chr17:19564634-19564635
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr17:19564458-19564820	HepG2	liver:	n/a	chr17:19564627-19564642 chr17:19564627-19564638 chr17:19564627-19564638
2	MAFF	chr17:19564488-19564781	HepG2	liver:	n/a	chr17:19564625-19564643
3	MAFK	chr17:19564481-19564790	IMR90	lung:	n/a	chr17:19564627-19564642 chr17:19564627-19564638 chr17:19564627-19564638
4	MAFK	chr17:19564496-19564799	HepG2	liver:	n/a	chr17:19564627-19564642 chr17:19564627-19564638 chr17:19564627-19564638

No.	Distal block	Cell Line	Cell type
1	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
2	chr17:19564551..19566163-chr17:19566583..19568566,2	MCF-7	breast:
3	chr17:19558329..19562006-chr17:19563141..19565959,3	MCF-7	breast:
4	chr17:19552711..19555521-chr17:19564350..19566731,2	MCF-7	breast:

Variant related genes	Relation type
ALDH3A2	TF binding region
ENSG00000252349	TF binding region
ENSG00000264932	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1004491	0.86[CHD][hapmap]
rs1025904	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1034896	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204407	0.86[CHD][hapmap]
rs11650399	0.94[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11653348	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12453452	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453474	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602112	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12603959	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12937179	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938816	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949521	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1806922	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2072331	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072332	0.86[CHD][hapmap]
rs2072333	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245724	0.81[EUR][1000 genomes]
rs2386144	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2891952	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34943952	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35797108	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35852749	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760486	1.00[YRI][hapmap]
rs3760487	1.00[YRI][hapmap]
rs3786038	0.84[CHD][hapmap]
rs4598966	0.82[EUR][1000 genomes]
rs4646793	0.86[CHD][hapmap]
rs4646797	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925041	0.84[CHD][hapmap]
rs66462929	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71369434	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7223468	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7503517	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8064748	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8068713	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8073053	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8080672	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962801	0.86[CHD][hapmap]
rs9797254	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9909440	1.00[AFR][1000 genomes];0.99[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1800869	SMCR7	cis	cerebellum	SCAN
rs1800869	FLJ10847	cis	multi-tissue	Pritchard
rs1800869	ALDH3A2	cis	cerebellum	SCAN
rs1800869	TOM1L2	cis	parietal	SCAN
rs1800869	ALDH3A2	cis	multi-tissue	Pritchard
rs1800869	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs1800869	MED9	cis	parietal	SCAN
rs1800869	ALDH3A2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
2	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:19555000-19568800	Weak transcription	NH-A	brain
7	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
9	chr17:19555200-19566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:19555200-19566600	Weak transcription	NHDF-Ad	bronchial
11	chr17:19555200-19569800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:19555400-19570000	Strong transcription	Fetal Muscle Leg	muscle
14	chr17:19555600-19567200	Weak transcription	Right Atrium	heart
15	chr17:19555600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
17	chr17:19556200-19569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:19556600-19569800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:19557200-19569800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:19558200-19568200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:19558200-19569400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr17:19558200-19569600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:19558200-19569800	Strong transcription	Fetal Intestine Large	intestine
24	chr17:19558400-19566600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:19558400-19566800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:19558400-19567200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:19558400-19571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:19558600-19569800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr17:19558800-19566800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr17:19559200-19571800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:19559200-19574200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:19559400-19566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:19559400-19575000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr17:19559400-19575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:19559600-19570800	Strong transcription	Brain Anterior Caudate	brain
37	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:19559800-19564800	Weak transcription	Ovary	ovary
39	chr17:19559800-19565200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr17:19559800-19565400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr17:19560000-19564800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr17:19560000-19564800	Weak transcription	Osteobl	bone
44	chr17:19560000-19565400	Weak transcription	Colon Smooth Muscle	Colon
45	chr17:19560000-19565600	Weak transcription	HSMM	muscle
46	chr17:19560200-19565400	Weak transcription	Brain Angular Gyrus	brain
47	chr17:19560200-19565400	Weak transcription	Fetal Kidney	kidney
48	chr17:19560200-19566600	Weak transcription	Fetal Brain Male	brain
49	chr17:19560200-19566800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:19560200-19566800	Weak transcription	Right Ventricle	heart

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