Variant report

Variant	rs8824
Chromosome Location	chr1:186390303-186390304
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186381482..186384419-chr1:186389970..186392449,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10494586	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10911855	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16825295	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1919198	0.80[EUR][1000 genomes]
rs2026187	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2037830	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2141393	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2178215	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2383476	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2976253	0.80[ASN][1000 genomes]
rs3115761	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3124814	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3131550	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131551	0.83[AMR][1000 genomes]
rs3131558	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3766706	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3766708	0.80[AMR][1000 genomes]
rs3766709	0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes]
rs6425026	0.80[AMR][1000 genomes]
rs6700930	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap]
rs7756	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs878041	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv872589	chr1:186354146-186390303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv1824284	chr1:186358588-186441585	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8824	C1orf27	cis	multi-tissue	Pritchard
rs8824	H2AFJ	trans	brain	seeQTL
rs8824	ENSG00000157181	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186345400-186390600	Weak transcription	Small Intestine	intestine
2	chr1:186345400-186398200	Weak transcription	Spleen	Spleen
3	chr1:186362400-186405600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:186362800-186405600	Weak transcription	Right Ventricle	heart
5	chr1:186365600-186395200	Weak transcription	Psoas Muscle	Psoas
6	chr1:186366200-186393800	Weak transcription	Lung	lung
7	chr1:186368600-186398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:186372000-186391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:186372000-186392000	Weak transcription	Esophagus	oesophagus
10	chr1:186372000-186398200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:186372000-186406000	Weak transcription	Pancreas	Pancrea
12	chr1:186374800-186390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:186376800-186391800	Weak transcription	HepG2	liver
14	chr1:186376800-186399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:186379200-186395200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:186379400-186391200	Weak transcription	Fetal Kidney	kidney
17	chr1:186380000-186398800	Weak transcription	Brain Germinal Matrix	brain
18	chr1:186381400-186390600	Weak transcription	NHLF	lung
19	chr1:186381600-186391800	Weak transcription	Placenta	Placenta
20	chr1:186383000-186391200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:186386200-186390400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:186386400-186390800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:186386600-186390800	Strong transcription	Adipose Nuclei	Adipose
24	chr1:186386800-186390400	Strong transcription	HSMM	muscle
25	chr1:186387400-186390400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:186387400-186390400	Strong transcription	Liver	Liver
27	chr1:186387400-186390800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:186387600-186390800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:186387800-186390400	Strong transcription	HMEC	breast
30	chr1:186387800-186390800	Strong transcription	Dnd41	blood
31	chr1:186388000-186390400	Strong transcription	NHEK	skin
32	chr1:186388000-186390600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr1:186388600-186399400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:186388600-186404600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:186388600-186408000	Weak transcription	Fetal Brain Female	brain
36	chr1:186388600-186411600	Weak transcription	A549	lung
37	chr1:186388600-186417400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:186388800-186390400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:186388800-186390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:186388800-186390800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:186388800-186391800	Weak transcription	Primary B cells from cord blood	blood
42	chr1:186388800-186393400	Weak transcription	Fetal Heart	heart
43	chr1:186388800-186394800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:186388800-186396400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:186388800-186397400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:186388800-186405800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:186388800-186409400	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:186388800-186409400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:186389000-186390600	Weak transcription	Ovary	ovary
50	chr1:186389000-186391200	Weak transcription	H1 Cell Line	embryonic stem cell

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