Variant report

Variant	rs12937179
Chromosome Location	chr17:19584085-19584086
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19578904..19580816-chr17:19583999..19586179,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1004491	0.82[CHD][hapmap]
rs1025904	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1034896	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204407	0.82[CHD][hapmap]
rs11650399	0.94[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11653348	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11658227	0.84[CHB][hapmap]
rs12453452	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12453474	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12602112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12603959	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938816	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12949521	0.94[CEU][hapmap];0.82[AMR][1000 genomes]
rs1800869	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]
rs1806922	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2072331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072332	0.82[CHD][hapmap]
rs2072333	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2386144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2891952	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34943952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35797108	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35852749	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4598966	0.81[EUR][1000 genomes]
rs4646793	0.82[CHD][hapmap]
rs4646797	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646798	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66462929	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71369434	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7223468	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72840391	0.81[AMR][1000 genomes]
rs7503517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8064748	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8068713	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8073053	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8080672	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs962801	0.82[CHD][hapmap]
rs9797254	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9909440	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12937179	ALDH3A2	cis	multi-tissue	Pritchard
rs12937179	ALDH3A2	cis	lymphoblastoid	seeQTL
rs12937179	SMCR7	cis	cerebellum	SCAN
rs12937179	TOM1L2	cis	parietal	SCAN
rs12937179	ALDH3A2	cis	cerebellum	SCAN
rs12937179	FLJ10847	cis	multi-tissue	Pritchard
rs12937179	MED9	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
3	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
4	chr17:19575000-19590200	Weak transcription	Right Ventricle	heart
5	chr17:19575400-19585400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr17:19575800-19584600	Weak transcription	HSMM	muscle
7	chr17:19575800-19586600	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:19576000-19584600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:19576000-19596200	Weak transcription	Fetal Heart	heart
10	chr17:19577200-19585200	Strong transcription	Fetal Brain Female	brain
11	chr17:19578400-19585000	Strong transcription	Stomach Smooth Muscle	stomach
12	chr17:19578800-19585200	Strong transcription	Fetal Stomach	stomach
13	chr17:19580400-19584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:19580400-19584800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:19580600-19584400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr17:19580600-19585200	Weak transcription	Primary T cells from cord blood	blood
17	chr17:19580600-19586600	Weak transcription	Colonic Mucosa	Colon
18	chr17:19580600-19586600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:19580600-19589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:19580800-19585200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
21	chr17:19580800-19586800	Weak transcription	Fetal Intestine Large	intestine
22	chr17:19580800-19589600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:19581000-19584600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr17:19581000-19584800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:19581600-19584600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr17:19581600-19584600	Strong transcription	A549	lung
27	chr17:19581800-19584600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr17:19582400-19585200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr17:19582600-19584400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:19582600-19586000	Weak transcription	Left Ventricle	heart
31	chr17:19582600-19594800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:19582600-19605600	Weak transcription	Fetal Kidney	kidney
33	chr17:19582800-19584400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:19582800-19584400	Weak transcription	HMEC	breast
35	chr17:19582800-19584600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:19582800-19584600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr17:19582800-19584600	Weak transcription	Pancreas	Pancrea
38	chr17:19582800-19584600	Weak transcription	HSMMtube	muscle
39	chr17:19582800-19584600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr17:19582800-19584800	Weak transcription	Osteobl	bone
41	chr17:19582800-19586200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:19582800-19586400	Weak transcription	Adipose Nuclei	Adipose
43	chr17:19582800-19586400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr17:19582800-19586800	Weak transcription	Spleen	Spleen
45	chr17:19582800-19587000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr17:19582800-19588600	Weak transcription	Esophagus	oesophagus
47	chr17:19582800-19589200	Weak transcription	Liver	Liver
48	chr17:19582800-19589600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:19582800-19589800	Weak transcription	HepG2	liver
50	chr17:19582800-19590000	Weak transcription	Gastric	stomach

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