Variant report

Variant	rs28477467
Chromosome Location	chr8:96032905-96032906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:96032900-96033050	GM12868	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:95907238..95908885-chr8:96031801..96033415,2	K562	blood:
2	chr8:95977560..95980300-chr8:96031568..96033219,2	MCF-7	breast:
3	chr8:96031972..96033668-chr8:96035592..96037179,2	MCF-7	breast:
4	chr8:96032678..96034884-chr8:96035365..96037674,4	K562	blood:
5	chr8:96022490..96024943-chr8:96031523..96033508,2	MCF-7	breast:
6	chr8:95905055..95911257-chr8:96032486..96039313,18	MCF-7	breast:
7	chr8:96026673..96028534-chr8:96030617..96033209,2	K562	blood:
8	chr8:95962646..95965102-chr8:96032516..96035099,2	MCF-7	breast:
9	chr8:95959565..95963058-chr8:96031680..96034201,4	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFAF6	TF binding region
ENSG00000156170	Chromatin interaction
ENSG00000253878	Chromatin interaction
ENSG00000175305	Chromatin interaction
ENSG00000164938	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10086541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092003	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10093594	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096455	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097930	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10098197	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098453	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10100089	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10103841	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10105437	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106491	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10111154	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111300	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10112230	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113545	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1031388	1.00[ASN][1000 genomes]
rs11774085	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11776189	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779506	0.93[ASN][1000 genomes]
rs11780931	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781001	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781040	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781619	0.90[EUR][1000 genomes]
rs11784178	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11786380	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11786878	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13279040	0.87[ASN][1000 genomes]
rs1545480	0.93[ASN][1000 genomes]
rs16917224	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16917233	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340536	0.90[EUR][1000 genomes]
rs2599711	0.93[ASN][1000 genomes]
rs2599713	1.00[ASN][1000 genomes]
rs2599714	1.00[ASN][1000 genomes]
rs2599715	1.00[ASN][1000 genomes]
rs2678823	1.00[ASN][1000 genomes]
rs2678829	0.93[ASN][1000 genomes]
rs28363725	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378156	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28406132	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28419772	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28440026	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28496357	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28616734	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28651964	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28712702	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34700722	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35518242	0.87[ASN][1000 genomes]
rs4323442	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56901035	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57925408	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61596977	0.89[EUR][1000 genomes]
rs6471505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471506	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6651271	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651272	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6985880	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6989862	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7002940	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7008542	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71532343	0.87[ASN][1000 genomes]
rs73276406	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276417	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276437	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276439	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276444	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812312	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7818688	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7826046	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7826196	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7832570	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7842703	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7842715	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9297950	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9297951	0.98[EUR][1000 genomes];1.00[ASN][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	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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28477467	C8orf38	Cis_1M	lymphoblastoid	RTeQTL
rs28477467	INTS8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96009000-96036400	Weak transcription	Spleen	Spleen
2	chr8:96023400-96036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:96024800-96036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:96026400-96033600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:96026800-96036400	Weak transcription	HMEC	breast
6	chr8:96029400-96033200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr8:96029600-96036400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:96029800-96036600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:96030200-96033000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr8:96030800-96033000	Enhancers	Primary B cells from cord blood	blood
11	chr8:96030800-96033000	Enhancers	Primary B cells from peripheral blood	blood
12	chr8:96031200-96033400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr8:96032000-96033200	Enhancers	Primary hematopoietic stem cells	blood
14	chr8:96032400-96033000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr8:96032600-96033000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:96032600-96033000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr8:96032600-96033000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:96032600-96033000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:96032600-96033000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr8:96032600-96033000	Enhancers	Fetal Thymus	thymus
21	chr8:96032600-96033000	Enhancers	Gastric	stomach
22	chr8:96032600-96033200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:96032600-96033200	Enhancers	Colon Smooth Muscle	Colon
24	chr8:96032600-96033200	Enhancers	Right Atrium	heart
25	chr8:96032600-96033400	Enhancers	Stomach Mucosa	stomach
26	chr8:96032600-96034200	Enhancers	Left Ventricle	heart
27	chr8:96032600-96034200	Enhancers	Pancreas	Pancrea
28	chr8:96032600-96034400	Enhancers	Liver	Liver
29	chr8:96032600-96034600	Enhancers	HepG2	liver
30	chr8:96032600-96036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:96032800-96033000	Enhancers	Esophagus	oesophagus
32	chr8:96032800-96033000	Enhancers	Lung	lung
33	chr8:96032800-96033000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr8:96032800-96033600	Enhancers	Psoas Muscle	Psoas
35	chr8:96032800-96033800	Enhancers	Adipose Nuclei	Adipose
36	chr8:96032800-96034200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr8:96032800-96036400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr8:96032800-96036400	Weak transcription	GM12878-XiMat	blood
39	chr8:96032800-96036600	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links