Variant report

Variant	rs12940014
Chromosome Location	chr17:17603317-17603318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17600627..17603876-chr17:17631337..17634332,3	K562	blood:
2	chr17:17599477..17603323-chr17:17655564..17658131,3	MCF-7	breast:
3	chr17:17591306..17603641-chr17:17622226..17637880,43	MCF-7	breast:
4	chr17:17601444..17604142-chr17:17605171..17608312,3	K562	blood:
5	chr17:17601352..17603729-chr17:17740230..17742410,2	K562	blood:

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11656775	0.86[JPT][hapmap]
rs2001884	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2350632	0.86[EUR][1000 genomes]
rs2350633	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4496218	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4925092	0.89[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4925093	0.89[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4925094	0.89[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4925096	0.81[EUR][1000 genomes]
rs4925102	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925104	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925105	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925109	0.86[JPT][hapmap]
rs6502613	0.92[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6502615	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs7208561	0.85[CEU][hapmap]
rs7214245	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7224617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224619	0.87[EUR][1000 genomes]
rs7224739	0.85[CEU][hapmap]
rs7225934	0.88[EUR][1000 genomes]
rs8065154	0.89[CEU][hapmap]
rs8075153	0.89[CEU][hapmap]
rs897457	0.88[EUR][1000 genomes]
rs941448	0.86[JPT][hapmap]
rs9897044	0.80[EUR][1000 genomes]
rs9897309	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9897596	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9900803	0.86[JPT][hapmap]
rs9904468	0.88[EUR][1000 genomes]
rs9906532	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9910411	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
7	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv907755	chr17:17581184-17610587	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
13	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv543241	chr17:17596222-17703059	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
19	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12940014	TOM1L2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17597400-17607000	Enhancers	Fetal Heart	heart
2	chr17:17598600-17607000	Enhancers	Fetal Lung	lung
3	chr17:17598800-17603400	Enhancers	Spleen	Spleen
4	chr17:17598800-17603600	Enhancers	Esophagus	oesophagus
5	chr17:17598800-17603600	Enhancers	Right Atrium	heart
6	chr17:17598800-17604400	Enhancers	Fetal Muscle Trunk	muscle
7	chr17:17598800-17604800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr17:17598800-17606800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr17:17598800-17608000	Enhancers	Lung	lung
10	chr17:17598800-17608000	Enhancers	Pancreas	Pancrea
11	chr17:17598800-17608200	Enhancers	Left Ventricle	heart
12	chr17:17599000-17603400	Enhancers	Brain Hippocampus Middle	brain
13	chr17:17599000-17603400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr17:17599000-17603400	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr17:17599000-17603600	Enhancers	Brain Cingulate Gyrus	brain
16	chr17:17599000-17603600	Enhancers	Right Ventricle	heart
17	chr17:17599000-17603800	Enhancers	Adipose Nuclei	Adipose
18	chr17:17599000-17604400	Enhancers	Fetal Muscle Leg	muscle
19	chr17:17599000-17605800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr17:17599000-17606000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr17:17599200-17604000	Enhancers	Primary hematopoietic stem cells	blood
22	chr17:17599200-17607400	Enhancers	Stomach Mucosa	stomach
23	chr17:17599200-17615600	Weak transcription	Primary B cells from cord blood	blood
24	chr17:17599400-17603400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:17599400-17603400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:17599400-17603400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:17599400-17603400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:17599400-17603600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:17599400-17604000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr17:17599400-17605800	Weak transcription	Thymus	Thymus
31	chr17:17599400-17617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:17599400-17617400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr17:17599600-17607000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:17599600-17612400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:17599800-17604600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr17:17600000-17603600	Enhancers	Fetal Thymus	thymus
37	chr17:17600000-17604200	Enhancers	HMEC	breast
38	chr17:17600200-17603400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:17600400-17603400	Enhancers	Colonic Mucosa	Colon
40	chr17:17600400-17604600	Weak transcription	Dnd41	blood
41	chr17:17600400-17606800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr17:17600400-17614800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr17:17600600-17603400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr17:17600800-17604600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:17601000-17603400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
46	chr17:17601000-17603400	Weak transcription	Fetal Brain Female	brain
47	chr17:17601000-17603800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr17:17601000-17604800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:17601000-17605200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
50	chr17:17601000-17606000	Enhancers	Fetal Brain Male	brain

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