Variant report

Variant	rs12942065
Chromosome Location	chr17:19609947-19609948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19605469..19607365-chr17:19608848..19610393,2	MCF-7	breast:
2	chr17:19608389..19613191-chr17:19615280..19617422,4	MCF-7	breast:
3	chr17:19607572..19613783-chr17:19615236..19620972,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180638	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1006554	0.93[ASN][1000 genomes]
rs11204411	0.81[CEU][hapmap]
rs11204412	0.81[CEU][hapmap]
rs11204413	0.93[ASN][1000 genomes]
rs11204414	0.90[ASN][1000 genomes]
rs12945122	0.81[CEU][hapmap]
rs12948209	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948735	0.93[ASN][1000 genomes]
rs157404	0.86[JPT][hapmap]
rs2108967	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs281357	0.86[JPT][hapmap]
rs3744693	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4646784	1.00[CHB][hapmap]
rs4646787	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4924793	0.93[ASN][1000 genomes]
rs4925044	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7209418	0.81[CEU][hapmap]
rs7212752	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7214841	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7221211	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7222877	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8064572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs887241	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9898022	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9910370	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][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	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
2	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
3	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
4	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
5	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
6	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	21 gene(s)	inside rSNPs	diseases
8	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12942065	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19605800-19610800	Enhancers	Fetal Muscle Leg	muscle
2	chr17:19606200-19610800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr17:19606200-19613600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr17:19606400-19610600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:19607200-19610400	Weak transcription	Brain Anterior Caudate	brain
6	chr17:19607200-19610600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr17:19607200-19619800	Weak transcription	Spleen	Spleen
8	chr17:19607400-19610200	Weak transcription	Fetal Intestine Large	intestine
9	chr17:19607600-19611000	Weak transcription	Gastric	stomach
10	chr17:19607600-19627400	Weak transcription	Right Atrium	heart
11	chr17:19607800-19610200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:19607800-19612600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:19608000-19611000	Weak transcription	Stomach Mucosa	stomach
14	chr17:19608200-19617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:19608400-19610200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:19608600-19610400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr17:19608800-19619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr17:19609000-19610600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr17:19609000-19611000	Enhancers	Fetal Heart	heart
20	chr17:19609200-19610000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:19609200-19611400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:19609400-19610000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:19609400-19610200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:19609400-19610400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:19609400-19610400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:19609400-19610800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr17:19609400-19610800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:19609400-19610800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:19609400-19611000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr17:19609400-19612600	Enhancers	Esophagus	oesophagus
31	chr17:19609600-19610200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:19609600-19610600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr17:19609600-19610800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:19609600-19611000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr17:19609600-19611200	Enhancers	Placenta	Placenta
36	chr17:19609600-19611600	Enhancers	HMEC	breast
37	chr17:19609800-19610000	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr17:19609800-19610400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr17:19609800-19611600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:19609800-19611800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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