Variant report

Variant	rs2459965
Chromosome Location	chr8:95940800-95940801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95908677..95910544-chr8:95940800..95943519,2	MCF-7	breast:
2	chr8:95938390..95942310-chr8:95942961..95947841,5	MCF-7	breast:
3	chr8:95905785..95909727-chr8:95939984..95942423,3	MCF-7	breast:
4	chr8:95940317..95943070-chr8:95944968..95947278,2	MCF-7	breast:
5	chr8:95937992..95941627-chr8:95953308..95955835,4	MCF-7	breast:
6	chr8:95938382..95942226-chr8:95942291..95944810,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175305	Chromatin interaction
ENSG00000156170	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1017634	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956930	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs1971212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013995	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123647	0.89[ASW][hapmap];0.81[LWK][hapmap]
rs2253173	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2459963	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2459964	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2466431	0.92[ASN][1000 genomes]
rs2467672	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467673	0.95[ASN][1000 genomes]
rs2467674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467675	0.97[ASN][1000 genomes]
rs2467676	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2515235	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515237	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945554	0.89[ASW][hapmap];0.91[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs36118131	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4570121	0.83[AFR][1000 genomes]
rs4735330	0.83[AFR][1000 genomes]
rs4735331	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs4735332	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs6987400	0.83[AFR][1000 genomes]
rs7001535	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs7015841	0.89[ASW][hapmap];0.98[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs7017487	0.89[ASW][hapmap];0.98[LWK][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs7760	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs896849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643352	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv891203	chr8:95883232-95948202	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv891204	chr8:95883232-95965135	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2459965	C8orf38	cis	parietal	SCAN

Chromatin state (count:131 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95909400-95941000	Weak transcription	Ovary	ovary
2	chr8:95909400-95941200	Weak transcription	Fetal Stomach	stomach
3	chr8:95909600-95941800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr8:95918600-95947400	Weak transcription	Small Intestine	intestine
5	chr8:95919000-95941200	Weak transcription	Left Ventricle	heart
6	chr8:95919200-95948600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:95926200-95946400	Weak transcription	Stomach Mucosa	stomach
8	chr8:95926400-95941200	Weak transcription	Pancreas	Pancrea
9	chr8:95928600-95941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:95928600-95941200	Weak transcription	Fetal Intestine Small	intestine
11	chr8:95930200-95941800	Weak transcription	Spleen	Spleen
12	chr8:95930600-95940800	Weak transcription	Aorta	Aorta
13	chr8:95930600-95948600	Weak transcription	Gastric	stomach
14	chr8:95931800-95950000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr8:95933000-95941200	Weak transcription	Esophagus	oesophagus
16	chr8:95933400-95960600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr8:95933600-95940800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:95933600-95941200	Weak transcription	K562	blood
19	chr8:95933600-95942000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:95933600-95949600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:95933800-95941400	Weak transcription	Fetal Heart	heart
22	chr8:95934000-95940800	Weak transcription	Brain Hippocampus Middle	brain
23	chr8:95934200-95941400	Weak transcription	Right Ventricle	heart
24	chr8:95935200-95956400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:95935400-95941200	Weak transcription	HepG2	liver
26	chr8:95935600-95941200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr8:95935800-95952000	Weak transcription	NHEK	skin
28	chr8:95936000-95941000	Weak transcription	HUVEC	blood vessel
29	chr8:95936000-95941200	Weak transcription	Colon Smooth Muscle	Colon
30	chr8:95936000-95942600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:95936400-95941200	Strong transcription	Liver	Liver
32	chr8:95936400-95956800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:95936800-95941200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr8:95936800-95942200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:95936800-95946000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr8:95937000-95956800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr8:95937200-95940800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr8:95937200-95941200	Strong transcription	Fetal Thymus	thymus
39	chr8:95937200-95946000	Strong transcription	Placenta	Placenta
40	chr8:95937200-95953400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:95937200-95956000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr8:95937400-95941800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr8:95937400-95946200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr8:95937400-95950800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr8:95937600-95941800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr8:95938000-95943400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:95938200-95940800	Strong transcription	Primary B cells from cord blood	blood
48	chr8:95938200-95941000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr8:95938400-95943800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr8:95938400-95954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links