Variant report

Variant	rs890515
Chromosome Location	chr8:67371834-67371835
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr8:67371295-67372226	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr8:67371796-67372650	A549	lung:	n/a	chr8:67372173-67372194
3	MYC	chr8:67371286-67372294	MCF10A-Er-Src	breast:	n/a	chr8:67371585-67371594
4	RAD21	chr8:67371780-67372766	SK-N-SH	brain:	n/a	chr8:67372172-67372191
5	MYC	chr8:67371397-67372205	MCF10A-Er-Src	breast:	n/a	chr8:67371585-67371594
6	CTCF	chr8:67371790-67372533	HCT-116	colon:	n/a	chr8:67372173-67372194
7	CTCF	chr8:67371740-67371890	AG04449	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:67371423..67376205-chr8:67520601..67527002,8	MCF-7	breast:
2	chr8:67370489..67372991-chr8:67834453..67837306,2	MCF-7	breast:

Variant related genes	Relation type
C8orf46	TF binding region
ENSG00000254341	Chromatin interaction
ENSG00000245910	Chromatin interaction
ENSG00000185697	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1025228	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1030419	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1060242	0.87[EUR][1000 genomes]
rs10957372	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs1108	0.87[EUR][1000 genomes]
rs12541098	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs13682	0.87[EUR][1000 genomes]
rs1426907	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1426908	0.84[CHB][hapmap]
rs1963852	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2059640	0.87[EUR][1000 genomes]
rs2059641	0.87[EUR][1000 genomes]
rs2059642	0.87[EUR][1000 genomes]
rs2357894	0.81[EUR][1000 genomes]
rs2465982	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2465984	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2465985	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2465986	0.82[ASN][1000 genomes]
rs2465987	0.82[ASN][1000 genomes]
rs2465990	0.87[EUR][1000 genomes]
rs2555565	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2555569	0.87[EUR][1000 genomes]
rs2555570	0.87[EUR][1000 genomes]
rs2555571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2555572	0.87[EUR][1000 genomes]
rs2555574	0.87[EUR][1000 genomes]
rs2555575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2555582	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2555587	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2718988	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718990	0.95[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2719000	0.87[EUR][1000 genomes]
rs2719002	0.84[EUR][1000 genomes]
rs2719004	0.87[EUR][1000 genomes]
rs2719005	0.87[EUR][1000 genomes]
rs2719006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7005366	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs753082	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9693689	1.00[CEU][hapmap];0.89[JPT][hapmap]

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	esv3446467	chr8:66749863-67667068	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3414665	chr8:66936816-67381935	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv6236	chr8:67359312-67403981	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs890515	C8orf46	cis	Thyroid	GTEx
rs890515	C8orf46	cis	Esophagus Muscularis	GTEx
rs890515	C8orf46	cis	Artery Tibial	GTEx
rs890515	C8orf46	cis	Adipose Subcutaneous	GTEx
rs890515	C8orf46	cis	lung	GTEx
rs890515	ADHFE1	cis	Muscle Skeletal	GTEx
rs890515	C8orf46	cis	Stomach	GTEx
rs890515	ADHFE1	cis	Nerve Tibial	GTEx
rs890515	C8orf46	cis	Nerve Tibial	GTEx
rs890515	C8orf46	cis	Skin Sun Exposed Lower leg	GTEx
rs890515	ADHFE1	cis	Artery Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:67353600-67372400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:67356200-67374400	Strong transcription	Liver	Liver
3	chr8:67359000-67372200	Weak transcription	HSMMtube	muscle
4	chr8:67359400-67384400	Weak transcription	Fetal Kidney	kidney
5	chr8:67361200-67373800	Strong transcription	Fetal Intestine Small	intestine
6	chr8:67361400-67377400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:67361600-67374400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:67364400-67375800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:67364600-67373400	Weak transcription	Spleen	Spleen
10	chr8:67364600-67378800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr8:67364800-67384000	Weak transcription	Colon Smooth Muscle	Colon
12	chr8:67365200-67374600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr8:67365200-67377400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr8:67365400-67372400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr8:67365400-67383800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr8:67365600-67372200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:67365600-67372200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:67365600-67375400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:67365800-67372400	Weak transcription	Brain Angular Gyrus	brain
20	chr8:67365800-67379600	Weak transcription	Esophagus	oesophagus
21	chr8:67366000-67372200	Weak transcription	Brain Anterior Caudate	brain
22	chr8:67366000-67373400	Weak transcription	Gastric	stomach
23	chr8:67366000-67374000	Weak transcription	Right Ventricle	heart
24	chr8:67366000-67376600	Weak transcription	Right Atrium	heart
25	chr8:67366400-67372200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr8:67366400-67372200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:67366400-67373400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr8:67367600-67372200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr8:67368000-67372200	Weak transcription	Brain Substantia Nigra	brain
30	chr8:67368200-67372600	Weak transcription	Left Ventricle	heart
31	chr8:67368400-67384400	Weak transcription	Psoas Muscle	Psoas
32	chr8:67368800-67372400	Weak transcription	Ovary	ovary
33	chr8:67368800-67374000	Weak transcription	Fetal Intestine Large	intestine
34	chr8:67369000-67372200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr8:67369000-67372200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr8:67369000-67372200	Weak transcription	HSMM	muscle
37	chr8:67369000-67372200	Weak transcription	NHLF	lung
38	chr8:67369000-67373400	Weak transcription	Lung	lung
39	chr8:67369000-67375400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr8:67369000-67375800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr8:67369000-67376000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:67369000-67376000	Weak transcription	Fetal Heart	heart
43	chr8:67369200-67372000	Weak transcription	NHDF-Ad	bronchial
44	chr8:67369200-67372200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr8:67369200-67372200	Weak transcription	NH-A	brain
46	chr8:67369400-67372200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr8:67369400-67372600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr8:67369400-67373200	Weak transcription	Fetal Muscle Leg	muscle
49	chr8:67369600-67372000	Weak transcription	Brain Hippocampus Middle	brain
50	chr8:67369600-67372200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links