Variant report

Variant	rs9315678
Chromosome Location	chr13:39943803-39943804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39943129..39945538-chr13:39980519..39982065,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs6563698	0.82[GIH][hapmap]
rs6563700	0.89[AFR][1000 genomes]
rs7318557	0.82[GIH][hapmap]
rs9315679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532374	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548747	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39937200-39945400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:39938800-39944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr13:39938800-39944600	Weak transcription	Brain Anterior Caudate	brain
4	chr13:39939400-39944600	Weak transcription	Fetal Brain Female	brain
5	chr13:39939600-39944200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:39939600-39944200	Weak transcription	Brain Hippocampus Middle	brain
7	chr13:39939600-39944200	Weak transcription	Brain Substantia Nigra	brain
8	chr13:39939600-39944200	Weak transcription	Left Ventricle	heart
9	chr13:39939600-39944600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:39939600-39959600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr13:39939800-39944200	Weak transcription	NHEK	skin
12	chr13:39939800-39944400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:39939800-39944800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr13:39939800-39945000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr13:39939800-39959800	Weak transcription	Fetal Lung	lung
16	chr13:39940000-39944200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:39940000-39944200	Weak transcription	Fetal Muscle Leg	muscle
18	chr13:39940000-39944400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:39940000-39944400	Weak transcription	Right Ventricle	heart
20	chr13:39940000-39944400	Weak transcription	HMEC	breast
21	chr13:39940000-39944600	Weak transcription	NHLF	lung
22	chr13:39940000-39944800	Weak transcription	Aorta	Aorta
23	chr13:39940200-39944600	Weak transcription	HSMMtube	muscle
24	chr13:39940200-39947400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:39940200-39953800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:39940600-39944400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:39940600-39953800	Weak transcription	Osteobl	bone
28	chr13:39941000-39944200	Weak transcription	NHDF-Ad	bronchial
29	chr13:39941000-39944600	Weak transcription	Ovary	ovary
30	chr13:39941000-39946400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:39941400-39947000	Weak transcription	Right Atrium	heart
32	chr13:39942600-39946000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:39943200-39953800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:39943600-39944000	Weak transcription	Colon Smooth Muscle	Colon
35	chr13:39943600-39944600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:39943800-39947800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr13:39943800-39947800	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links