Variant report

Variant	rs9568300
Chromosome Location	chr13:50241792-50241793
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	chr13:50240420..50241989-chr13:50245723..50247987,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs9316472	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9562909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562910	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9562911	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9568299	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9568301	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9591290	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9596166	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9596170	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9596171	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9568300	EBPL	cis	Thyroid	GTEx
rs9568300	EBPL	cis	parietal	SCAN
rs9568300	EBPL	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50220000-50245400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr13:50224600-50243000	Weak transcription	Brain Germinal Matrix	brain
3	chr13:50224600-50252600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:50226400-50244000	Weak transcription	Colon Smooth Muscle	Colon
5	chr13:50227400-50253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:50228600-50242000	Weak transcription	HSMMtube	muscle
7	chr13:50228600-50244000	Weak transcription	Fetal Kidney	kidney
8	chr13:50229800-50243400	Weak transcription	Small Intestine	intestine
9	chr13:50230200-50242000	Weak transcription	NHDF-Ad	bronchial
10	chr13:50230400-50243400	Strong transcription	Fetal Stomach	stomach
11	chr13:50231000-50246800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr13:50231200-50241800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:50231400-50241800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:50231400-50243000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:50231800-50241800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr13:50232200-50242400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:50232800-50241800	Weak transcription	Brain Substantia Nigra	brain
19	chr13:50233000-50242600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:50233400-50242000	Strong transcription	Liver	Liver
21	chr13:50233600-50242400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr13:50233600-50242600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr13:50233800-50242400	Strong transcription	Dnd41	blood
24	chr13:50234200-50244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr13:50234400-50243600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:50234400-50245400	Weak transcription	Psoas Muscle	Psoas
27	chr13:50234600-50242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:50235400-50252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
30	chr13:50236000-50244000	Weak transcription	Brain Anterior Caudate	brain
31	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr13:50237400-50256000	Weak transcription	NH-A	brain
33	chr13:50238800-50241800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr13:50238800-50253000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr13:50239000-50242400	Strong transcription	Fetal Intestine Small	intestine
36	chr13:50239400-50241800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:50239400-50243800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr13:50239600-50242200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr13:50239600-50242200	Strong transcription	NHEK	skin
40	chr13:50239600-50242400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:50239800-50241800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr13:50239800-50242000	Strong transcription	Brain Hippocampus Middle	brain
43	chr13:50239800-50242000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:50239800-50242200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr13:50239800-50242200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:50239800-50242200	Strong transcription	Fetal Thymus	thymus
47	chr13:50239800-50242200	Strong transcription	Pancreas	Pancrea
48	chr13:50239800-50242200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr13:50239800-50242200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr13:50239800-50242200	Strong transcription	HUVEC	blood vessel

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