Variant report

Variant	rs11164825
Chromosome Location	chr1:93311707-93311708
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	chr1:93303345..93305385-chr1:93311213..93313203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251795	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10874745	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11582791	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11586089	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11586570	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12062315	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12082659	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12726286	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12728322	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12738654	0.83[EUR][1000 genomes]
rs12746956	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12750269	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1854797	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2893226	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34041593	0.83[EUR][1000 genomes]
rs34098754	0.85[EUR][1000 genomes]
rs34168045	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34244251	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35031391	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35051335	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35183060	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58270016	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6604026	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525381	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6657809	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6687931	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71652510	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7514280	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7521417	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7554594	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11164825	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93300400-93316000	Strong transcription	Primary B cells from cord blood	blood
2	chr1:93301000-93318400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr1:93303000-93317200	Weak transcription	Right Ventricle	heart
4	chr1:93304200-93312200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:93304400-93349000	Weak transcription	Aorta	Aorta
6	chr1:93305000-93312000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:93305200-93317200	Weak transcription	Fetal Heart	heart
8	chr1:93305800-93316200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:93306000-93311800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:93306000-93312000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:93306000-93316800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:93306000-93317200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:93306400-93312200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:93306400-93313800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:93306400-93317200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:93306600-93317400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:93306800-93324800	Weak transcription	Pancreas	Pancrea
18	chr1:93307000-93316600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:93307000-93324800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:93307200-93312200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:93307200-93320000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:93307800-93316800	Weak transcription	Fetal Lung	lung
23	chr1:93308000-93323400	Weak transcription	Small Intestine	intestine
24	chr1:93308000-93324600	Weak transcription	Psoas Muscle	Psoas
25	chr1:93308400-93313400	Weak transcription	Stomach Mucosa	stomach
26	chr1:93309200-93317400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:93309400-93324800	Weak transcription	NHDF-Ad	bronchial
28	chr1:93309600-93314000	Weak transcription	Hela-S3	cervix
29	chr1:93309600-93324800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:93309800-93312000	Weak transcription	HUVEC	blood vessel
31	chr1:93309800-93312400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:93309800-93313400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:93309800-93313400	Weak transcription	Colonic Mucosa	Colon
34	chr1:93309800-93313400	Weak transcription	Esophagus	oesophagus
35	chr1:93309800-93313400	Weak transcription	NHEK	skin
36	chr1:93309800-93314800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:93309800-93315000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:93309800-93315000	Weak transcription	Thymus	Thymus
39	chr1:93309800-93315400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:93309800-93317200	Weak transcription	K562	blood
41	chr1:93309800-93317400	Weak transcription	Ovary	ovary
42	chr1:93309800-93317400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:93309800-93317600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:93309800-93318200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:93309800-93320000	Weak transcription	Spleen	Spleen
46	chr1:93309800-93324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:93309800-93324400	Weak transcription	A549	lung
48	chr1:93309800-93324400	Weak transcription	Osteobl	bone
49	chr1:93309800-93342400	Weak transcription	NHLF	lung
50	chr1:93310000-93311800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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