Variant report

Variant	rs6669274
Chromosome Location	chr1:47088116-47088117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47087714..47088829-chr1:47190613..47191839,11	K562	blood:
2	chr1:47087884..47088399-chr1:47191014..47191583,2	MCF-7	breast:
3	chr1:47086033..47090385-chr1:47091411..47095597,5	K562	blood:
4	chr1:47087818..47089652-chr1:47106481..47108594,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11211328	0.83[TSI][hapmap]
rs11579762	0.96[EUR][1000 genomes]
rs12029680	0.83[TSI][hapmap]
rs1258008	0.81[EUR][1000 genomes]
rs12741355	0.96[EUR][1000 genomes]
rs12755846	0.96[EUR][1000 genomes]
rs1933934	0.86[TSI][hapmap]
rs3766231	0.83[TSI][hapmap]
rs4518838	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660948	0.96[EUR][1000 genomes]
rs6429606	0.83[TSI][hapmap]
rs6662520	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669160	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556481	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6669274	C1orf84	cis	cerebellum	SCAN
rs6669274	MKNK1	cis	lung	GTEx
rs6669274	CLDN19	cis	cerebellum	SCAN
rs6669274	ATPAF1	cis	multi-tissue	Pritchard
rs6669274	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs6669274	C1orf223	cis	parietal	SCAN
rs6669274	MOBKL2C	cis	cerebellum	SCAN
rs6669274	MKNK1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47082800-47089600	Weak transcription	Small Intestine	intestine
2	chr1:47083000-47090800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:47083000-47094400	Weak transcription	Primary T cells from cord blood	blood
4	chr1:47083000-47094600	Weak transcription	Right Ventricle	heart
5	chr1:47083000-47097200	Weak transcription	Gastric	stomach
6	chr1:47083000-47100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:47083200-47094400	Weak transcription	Brain Angular Gyrus	brain
8	chr1:47083200-47094600	Weak transcription	Liver	Liver
9	chr1:47083200-47095400	Weak transcription	Fetal Thymus	thymus
10	chr1:47083200-47095600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:47083200-47097200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:47083200-47097200	Weak transcription	Aorta	Aorta
13	chr1:47083200-47097200	Weak transcription	Thymus	Thymus
14	chr1:47083200-47100200	Weak transcription	Psoas Muscle	Psoas
15	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
16	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:47083400-47089200	Weak transcription	Right Atrium	heart
18	chr1:47083400-47092200	Weak transcription	Pancreas	Pancrea
19	chr1:47083400-47094200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:47083400-47094200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:47083400-47094600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:47083400-47094800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:47083400-47095000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:47083400-47095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:47083400-47095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:47083400-47095600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:47083400-47095600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:47083400-47096800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:47083400-47097000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:47083400-47097400	Weak transcription	Brain Substantia Nigra	brain
31	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:47083600-47094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:47084800-47094600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:47084800-47097000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:47085400-47089600	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:47085600-47099000	Weak transcription	GM12878-XiMat	blood
37	chr1:47085800-47097200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:47085800-47097600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:47087000-47088200	Enhancers	HSMM	muscle
40	chr1:47087000-47088400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:47087400-47088200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:47087400-47088200	Enhancers	Colonic Mucosa	Colon
43	chr1:47087400-47088200	Enhancers	Fetal Intestine Large	intestine
44	chr1:47087400-47088200	Enhancers	Osteobl	bone
45	chr1:47087400-47088800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:47087600-47088200	Enhancers	Stomach Smooth Muscle	stomach
47	chr1:47087600-47088200	Enhancers	HSMMtube	muscle
48	chr1:47087600-47088200	Enhancers	K562	blood
49	chr1:47087600-47088400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:47087600-47088400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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