Variant report

Variant	rs57925408
Chromosome Location	chr8:96062930-96062931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95906524..95908968-chr8:96061883..96064789,2	MCF-7	breast:
2	chr8:96060626..96064106-chr8:96144836..96147979,3	MCF-7	breast:
3	chr8:96053111..96056097-chr8:96061243..96063716,2	MCF-7	breast:
4	chr8:96050393..96052633-chr8:96061635..96064510,2	K562	blood:

Variant related genes	Relation type
ENSG00000156170	Chromatin interaction
ENSG00000175305	Chromatin interaction
ENSG00000175895	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10086541	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10092003	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10093594	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10096455	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10097930	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10098197	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10098453	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10100089	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10103841	0.85[EUR][1000 genomes]
rs10105437	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10106491	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10110635	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10111154	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10111300	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10112230	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10113545	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1031388	0.93[ASN][1000 genomes]
rs11774085	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11776189	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11779506	1.00[ASN][1000 genomes]
rs11780931	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11781001	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11781040	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11781619	0.86[EUR][1000 genomes]
rs11784178	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11786380	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11786878	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13279040	0.93[ASN][1000 genomes]
rs1545480	1.00[ASN][1000 genomes]
rs16917224	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16917233	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2340536	0.86[EUR][1000 genomes]
rs2599711	1.00[ASN][1000 genomes]
rs2599713	0.93[ASN][1000 genomes]
rs2599714	0.93[ASN][1000 genomes]
rs2599715	0.93[ASN][1000 genomes]
rs2678823	0.93[ASN][1000 genomes]
rs2678829	0.87[ASN][1000 genomes]
rs28363725	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28378156	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28406132	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28419772	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28440026	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28477467	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28496357	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28616734	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28651964	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28712702	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34700722	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35518242	0.93[ASN][1000 genomes]
rs4323442	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56901035	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61596977	0.85[EUR][1000 genomes]
rs6471505	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6471506	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6651271	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6651272	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6985880	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6989862	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7002940	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7008542	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71532343	0.93[ASN][1000 genomes]
rs73276406	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73276417	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73276437	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276439	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276444	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7812312	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7818688	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7826196	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7832570	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7842703	0.80[AMR][1000 genomes]
rs7842715	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9297950	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9297951	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv891205	chr8:96062601-96115476	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs57925408	C8orf38	Cis_1M	lymphoblastoid	RTeQTL
rs57925408	INTS8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96037800-96070200	Weak transcription	Aorta	Aorta
2	chr8:96038000-96063800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:96038200-96072400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:96038200-96080000	Weak transcription	Colonic Mucosa	Colon
5	chr8:96038400-96063600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:96038400-96066800	Weak transcription	Stomach Mucosa	stomach
7	chr8:96038400-96085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr8:96042800-96072200	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr8:96043600-96063600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr8:96044200-96071800	Strong transcription	Dnd41	blood
11	chr8:96044400-96063200	Strong transcription	Stomach Smooth Muscle	stomach
12	chr8:96044400-96066600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr8:96044400-96066800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr8:96044600-96065200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr8:96044800-96066600	Strong transcription	Fetal Thymus	thymus
16	chr8:96045000-96068800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:96045800-96064000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr8:96046400-96070200	Weak transcription	Gastric	stomach
19	chr8:96048400-96071800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:96050000-96063800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr8:96052000-96063800	Strong transcription	A549	lung
22	chr8:96052000-96064600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:96052000-96065000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr8:96052000-96065400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr8:96052200-96065800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr8:96052200-96070200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:96052400-96068200	Strong transcription	Liver	Liver
28	chr8:96052800-96063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr8:96052800-96065800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr8:96053000-96063600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr8:96053200-96063600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr8:96053400-96063400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr8:96053600-96063400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr8:96054000-96065800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr8:96055200-96064600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr8:96055200-96064800	Strong transcription	K562	blood
37	chr8:96055400-96063400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr8:96055400-96063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:96055400-96066600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr8:96055600-96063000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:96055600-96063800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:96056200-96068600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:96056400-96064200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr8:96057000-96063400	Strong transcription	HMEC	breast
45	chr8:96057000-96064800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:96057000-96065600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr8:96057400-96064400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr8:96057600-96063200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:96057600-96063800	Strong transcription	Placenta	Placenta
50	chr8:96058000-96063400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links