Variant report

Variant	rs28399241
Chromosome Location	chr8:8663215-8663216
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	chr8:8655376..8657753-chr8:8661368..8663526,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10088933	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11783966	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12547493	0.96[ASN][1000 genomes]
rs13260419	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13265731	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1473029	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4841043	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4841044	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4841047	0.87[EUR][1000 genomes]
rs6988939	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6993494	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7006589	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9329167	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1022511	chr8:8493992-8737132	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539457	chr8:8493992-8737132	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv1824870	chr8:8583943-8699382	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv610189	chr8:8590437-8664940	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv831228	chr8:8608387-8790790	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1018828	chr8:8609880-8790660	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv1022331	chr8:8610035-8787981	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28399241	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs28399241	SGK223	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8637600-8679800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:8649200-8666400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:8649400-8663600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:8649400-8663800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:8650800-8663400	Weak transcription	Hela-S3	cervix
6	chr8:8653800-8663400	Weak transcription	HMEC	breast
7	chr8:8653800-8674800	Weak transcription	Brain Germinal Matrix	brain
8	chr8:8654000-8663600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr8:8654000-8666800	Weak transcription	NHDF-Ad	bronchial
10	chr8:8654000-8666800	Weak transcription	NHLF	lung
11	chr8:8654000-8671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:8655000-8663400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:8655200-8663400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:8655200-8663600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:8655200-8663800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr8:8655200-8666400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr8:8655200-8680600	Weak transcription	Colonic Mucosa	Colon
18	chr8:8655400-8663600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:8655400-8663600	Weak transcription	HSMM	muscle
20	chr8:8655400-8666800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr8:8655600-8673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:8655600-8685600	Weak transcription	Fetal Brain Female	brain
23	chr8:8655800-8663600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:8655800-8666200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr8:8655800-8666800	Weak transcription	Fetal Brain Male	brain
26	chr8:8655800-8669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr8:8655800-8669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr8:8655800-8669200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr8:8655800-8669200	Weak transcription	Thymus	Thymus
30	chr8:8656000-8663600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:8656000-8669600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr8:8656200-8663600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr8:8656200-8667000	Weak transcription	Placenta	Placenta
34	chr8:8656200-8669000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:8656200-8669000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr8:8656400-8663600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr8:8656400-8663800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr8:8658000-8664800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr8:8658200-8663600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:8658200-8663600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr8:8658200-8663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr8:8658200-8666800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:8658200-8668800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr8:8658200-8669000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:8658400-8663400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr8:8658400-8663600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr8:8658400-8663600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr8:8658400-8663600	Weak transcription	Osteobl	bone
49	chr8:8658400-8663800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr8:8658400-8666400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links