Variant report

Variant	rs28405386
Chromosome Location	chr8:61325642-61325643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61324950..61327634-chr8:61427769..61429933,3	MCF-7	breast:
2	chr8:61324832..61325643-chr8:61526141..61526863,2	MCF-7	breast:
3	chr8:61309337..61310142-chr8:61324728..61325721,2	K562	blood:
4	chr8:61324855..61325726-chr8:61523264..61524233,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CA8-3	chr8:61325569-61326029	ENSG00000251396

Variant related genes	Relation type
ENSG00000104388	Chromatin interaction
ENSG00000251396	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10101576	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10101714	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10504311	0.98[ASN][1000 genomes]
rs10957135	0.98[ASN][1000 genomes]
rs10957136	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957137	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10957138	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957140	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957141	0.82[ASN][1000 genomes]
rs11774500	0.82[ASN][1000 genomes]
rs11775407	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11778708	0.82[ASN][1000 genomes]
rs11782463	0.82[ASN][1000 genomes]
rs11784284	0.82[ASN][1000 genomes]
rs13266707	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13267828	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13269925	0.82[ASN][1000 genomes]
rs1480342	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2326556	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2326557	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28542403	0.81[ASN][1000 genomes]
rs28678079	0.82[ASN][1000 genomes]
rs34775344	0.82[ASN][1000 genomes]
rs35837434	0.82[ASN][1000 genomes]
rs6471884	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66983460	0.80[ASN][1000 genomes]
rs6987523	0.82[ASN][1000 genomes]
rs6991529	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6995397	0.90[EUR][1000 genomes]
rs6996344	0.82[ASN][1000 genomes]
rs6998294	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7017556	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7820349	0.82[ASN][1000 genomes]
rs7822391	0.82[ASN][1000 genomes]
rs7826226	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7832664	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7832964	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7842105	0.91[EUR][1000 genomes];0.82[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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
2	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28405386	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61309000-61330000	Weak transcription	Right Atrium	heart
2	chr8:61324000-61327000	Enhancers	Fetal Heart	heart
3	chr8:61324800-61326000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:61324800-61327000	Enhancers	Placenta	Placenta
5	chr8:61325000-61326600	Active TSS	Brain Anterior Caudate	brain
6	chr8:61325200-61325800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr8:61325200-61325800	Enhancers	Colonic Mucosa	Colon
8	chr8:61325200-61326000	Enhancers	Primary B cells from cord blood	blood
9	chr8:61325200-61326000	Enhancers	Primary hematopoietic stem cells	blood
10	chr8:61325200-61326000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:61325200-61326000	Active TSS	Brain Cingulate Gyrus	brain
12	chr8:61325200-61326400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr8:61325200-61326400	Active TSS	Brain Angular Gyrus	brain
14	chr8:61325200-61326400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:61325200-61326600	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr8:61325200-61327000	Enhancers	Pancreas	Pancrea
17	chr8:61325200-61327200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr8:61325400-61325800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:61325400-61325800	Flanking Active TSS	A549	lung
20	chr8:61325400-61326000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr8:61325400-61326000	Flanking Active TSS	Fetal Brain Female	brain
22	chr8:61325400-61326200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:61325400-61326200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:61325400-61326200	Enhancers	Lung	lung
25	chr8:61325400-61326400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:61325400-61326400	Enhancers	Right Ventricle	heart
27	chr8:61325400-61326600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr8:61325400-61326600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr8:61325400-61327200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:61325400-61327200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr8:61325600-61325800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:61325600-61325800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr8:61325600-61325800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr8:61325600-61325800	Flanking Active TSS	Fetal Brain Male	brain
35	chr8:61325600-61325800	Bivalent Enhancer	Fetal Stomach	stomach
36	chr8:61325600-61325800	Enhancers	Spleen	Spleen
37	chr8:61325600-61325800	Enhancers	K562	blood
38	chr8:61325600-61325800	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr8:61325600-61325800	Active TSS	NH-A	brain
40	chr8:61325600-61326000	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr8:61325600-61326000	Active TSS	Gastric	stomach
42	chr8:61325600-61326200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr8:61325600-61326200	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr8:61325600-61326200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr8:61325600-61326200	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr8:61325600-61326200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr8:61325600-61326200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr8:61325600-61326200	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr8:61325600-61326400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr8:61325600-61326800	Active TSS	Brain Inferior Temporal Lobe	brain

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