Variant report

Variant	rs3742301
Chromosome Location	chr13:53422553-53422554
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	chr13:53226555..53228977-chr13:53419370..53422779,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11617253	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12100313	0.86[EUR][1000 genomes]
rs12100317	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1274580	0.87[EUR][1000 genomes]
rs1274581	0.87[EUR][1000 genomes]
rs1323118	0.85[EUR][1000 genomes]
rs1359046	0.86[ASN][1000 genomes]
rs2236363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764035	0.87[EUR][1000 genomes]
rs3742300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4143183	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886021	0.93[ASN][1000 genomes]
rs508523	0.87[EUR][1000 genomes]
rs540528	0.86[EUR][1000 genomes]
rs582583	0.84[ASN][1000 genomes]
rs61950421	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs646902	0.87[EUR][1000 genomes]
rs648146	0.86[EUR][1000 genomes]
rs649523	0.87[EUR][1000 genomes]
rs67683610	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7337857	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9788389	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788390	0.86[EUR][1000 genomes]
rs9788403	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900089	chr13:53385334-53429453	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv523092	chr13:53419139-53429453	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	esv14133	chr13:53419990-53422747	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv1794389	chr13:53420344-53423105	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv1834136	chr13:53420344-53423105	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv1845789	chr13:53420344-53423105	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv561669	chr13:53420344-53423105	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1842551	chr13:53420679-53423105	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv561676	chr13:53420843-53422553	Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3742301	RB1	cis	parietal	SCAN
rs3742301	LOC220429	cis	cerebellum	SCAN
rs3742301	EBPL	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53418800-53422800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:53418800-53422800	Enhancers	Pancreas	Pancrea
3	chr13:53419400-53422600	Bivalent Enhancer	Lung	lung
4	chr13:53419400-53422800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:53419400-53423000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr13:53419400-53423200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr13:53419400-53423200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr13:53419400-53423200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
9	chr13:53419600-53422600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr13:53419600-53422600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr13:53419600-53424400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr13:53419800-53422800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr13:53420000-53422800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
14	chr13:53420000-53423200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr13:53420000-53424000	ZNF genes & repeats	GM12878-XiMat	blood
16	chr13:53420800-53423400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:53421000-53423200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
18	chr13:53421000-53423400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
19	chr13:53421200-53422600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
20	chr13:53421200-53422600	ZNF genes & repeats	Gastric	stomach
21	chr13:53421200-53424800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr13:53421400-53422600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:53421400-53422600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
24	chr13:53421400-53423000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr13:53421400-53424400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
26	chr13:53421600-53422600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:53421600-53422600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:53421600-53422600	Bivalent Enhancer	Right Ventricle	heart
29	chr13:53421600-53423200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:53421600-53424400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr13:53421800-53426200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
32	chr13:53422000-53422600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:53422000-53423000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
34	chr13:53422000-53423400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
35	chr13:53422000-53423400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr13:53422200-53422600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr13:53422200-53422600	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:53422200-53422600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
39	chr13:53422200-53422600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
40	chr13:53422200-53422800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
41	chr13:53422200-53423000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr13:53422200-53423200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
43	chr13:53422200-53424600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
44	chr13:53422400-53422600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
45	chr13:53422400-53422600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
46	chr13:53422400-53422600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
47	chr13:53422400-53422600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:53422400-53422600	Flanking Active TSS	Fetal Brain Male	brain
49	chr13:53422400-53422600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
50	chr13:53422400-53422600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon

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