Variant report

Variant	rs13396048
Chromosome Location	chr2:62728105-62728106
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	chr2:62726106..62729574-chr2:62730789..62734406,4	MCF-7	breast:
2	chr2:62718276..62720526-chr2:62727319..62729124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241625	Chromatin interaction
ENSG00000186889	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10191324	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10191428	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11125927	0.91[EUR][1000 genomes]
rs11903221	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622031	0.83[JPT][hapmap]
rs13035295	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13388903	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13389363	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233979	0.84[CEU][hapmap];0.85[LWK][hapmap]
rs4286259	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4405748	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4672527	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672528	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57645001	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745280	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757222	0.92[ASN][1000 genomes]
rs6757448	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs73934251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73934252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73934253	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604354	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13396048	TMEM17	cis	parietal	SCAN
rs13396048	CEP68	cis	cerebellum	SCAN
rs13396048	CCT4	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62705800-62732200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:62713400-62732400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:62714200-62732400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:62714400-62728400	Weak transcription	HMEC	breast
5	chr2:62716600-62728200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:62716600-62732200	Weak transcription	Brain Angular Gyrus	brain
7	chr2:62716600-62732400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:62716800-62732000	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:62717200-62728800	Weak transcription	NHDF-Ad	bronchial
10	chr2:62717600-62732400	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:62717600-62732600	Weak transcription	Ovary	ovary
12	chr2:62719600-62732800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:62722600-62728800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:62723000-62732200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:62723200-62728400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:62723600-62728200	Weak transcription	A549	lung
17	chr2:62723600-62728600	Weak transcription	Adipose Nuclei	Adipose
18	chr2:62723600-62728800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:62723600-62732200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:62724600-62728200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:62725000-62732000	Weak transcription	Fetal Intestine Large	intestine
22	chr2:62725000-62732400	Weak transcription	Fetal Lung	lung
23	chr2:62725200-62728800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:62725200-62732200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:62725800-62728200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:62726400-62728400	Weak transcription	Fetal Brain Female	brain
27	chr2:62726400-62732400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:62726400-62732400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:62726600-62728200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:62726800-62732200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:62727000-62728800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:62727000-62728800	Weak transcription	NH-A	brain
33	chr2:62727200-62728600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:62727200-62732200	Weak transcription	Osteobl	bone
35	chr2:62727200-62732400	Weak transcription	HSMMtube	muscle
36	chr2:62727400-62728200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:62727400-62728600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:62728000-62728800	Enhancers	Fetal Intestine Small	intestine
39	chr2:62728000-62729200	Strong transcription	Brain Anterior Caudate	brain
40	chr2:62728000-62729800	Enhancers	HepG2	liver
41	chr2:62728000-62732200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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