Variant report

Variant	rs12453332
Chromosome Location	chr17:19969297-19969298
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19968366..19971669-chr17:19975346..19978393,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11204422	0.97[ASN][1000 genomes]
rs11869931	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870381	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11870673	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12449914	0.91[AMR][1000 genomes]
rs12451216	0.88[ASN][1000 genomes]
rs12451841	0.95[ASN][1000 genomes]
rs12937327	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12942179	0.97[ASN][1000 genomes]
rs12943904	0.89[AMR][1000 genomes]
rs12947713	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949710	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1468953	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17685923	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17686798	0.85[ASN][1000 genomes]
rs17759041	0.91[AMR][1000 genomes]
rs17759609	0.90[AMR][1000 genomes]
rs17759959	0.87[ASN][1000 genomes]
rs34370440	0.95[ASN][1000 genomes]
rs34756775	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35041742	0.82[ASN][1000 genomes]
rs35124809	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35156798	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35191778	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35244101	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35317166	0.94[AMR][1000 genomes]
rs35493088	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35770292	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35915823	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36051592	0.83[ASN][1000 genomes]
rs3862151	0.91[AMR][1000 genomes]
rs4341795	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4346259	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4350625	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4471741	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924802	0.94[AMR][1000 genomes]
rs4924808	0.88[ASN][1000 genomes]
rs4925071	0.91[AMR][1000 genomes]
rs4925074	0.91[AMR][1000 genomes]
rs4925075	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925076	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925078	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925082	0.95[ASN][1000 genomes]
rs4925084	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4925088	0.81[ASN][1000 genomes]
rs56371654	0.94[AMR][1000 genomes]
rs62067488	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215803	0.97[ASN][1000 genomes]
rs7503407	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066705	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8068484	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074791	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8075343	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081817	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs888424	0.97[ASN][1000 genomes]
rs972966	0.85[ASN][1000 genomes]
rs9901125	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12453332	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19966200-19970200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr17:19966400-19970000	Enhancers	Brain Angular Gyrus	brain
3	chr17:19966400-19970200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:19966400-19970400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:19966600-19969600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:19966600-19970000	Enhancers	Colon Smooth Muscle	Colon
7	chr17:19966800-19969800	Enhancers	Fetal Stomach	stomach
8	chr17:19967000-19970000	Enhancers	Fetal Muscle Leg	muscle
9	chr17:19967600-19970400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:19967800-19970400	Enhancers	NHEK	skin
11	chr17:19967800-19972400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:19968000-19969600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr17:19968000-19970000	Enhancers	Brain Anterior Caudate	brain
14	chr17:19968000-19970000	Enhancers	Brain Substantia Nigra	brain
15	chr17:19968000-19970000	Enhancers	NHLF	lung
16	chr17:19968000-19970200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:19968000-19970200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:19968000-19970200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:19968000-19970200	Enhancers	Hela-S3	cervix
20	chr17:19968000-19970200	Enhancers	Osteobl	bone
21	chr17:19968000-19970400	Enhancers	Adipose Nuclei	Adipose
22	chr17:19968000-19970400	Enhancers	HMEC	breast
23	chr17:19968000-19974800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:19968000-19977000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr17:19968200-19969400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr17:19968200-19969400	Weak transcription	HSMM	muscle
27	chr17:19968200-19969600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr17:19968200-19969600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:19968200-19969800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:19968200-19970000	Enhancers	GM12878-XiMat	blood
31	chr17:19968200-19970200	Enhancers	Brain Hippocampus Middle	brain
32	chr17:19968200-19970200	Weak transcription	K562	blood
33	chr17:19968200-19970200	Enhancers	NHDF-Ad	bronchial
34	chr17:19968200-19970400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:19968200-19972200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr17:19968200-19977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:19968400-19969400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr17:19968600-19969400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:19968600-19975400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:19968800-19970200	Enhancers	NH-A	brain
41	chr17:19969000-19969800	Enhancers	Fetal Lung	lung
42	chr17:19969000-19970000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:19969000-19975200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr17:19969000-19975600	Weak transcription	Lung	lung
45	chr17:19969000-19975600	Weak transcription	Right Atrium	heart
46	chr17:19969200-19969400	Enhancers	A549	lung
47	chr17:19969200-19969600	Weak transcription	Ovary	ovary
48	chr17:19969200-19970000	Enhancers	Brain Cingulate Gyrus	brain
49	chr17:19969200-19971000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr17:19969200-19971400	Weak transcription	Monocytes-CD14+_RO01746	blood

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