Variant report

Variant	rs6692443
Chromosome Location	chr1:224357620-224357621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10429876	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916393	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916405	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576822	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079996	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144944	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032003	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2172358	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2896985	0.81[JPT][hapmap]
rs3754091	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767728	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4359008	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4484894	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4528084	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56044078	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687334	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7520429	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7524705	0.80[JPT][hapmap]
rs7531891	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6692443	FBXO28	cis	multi-tissue	Pritchard
rs6692443	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224339200-224363200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:224345400-224363400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:224345600-224363400	Weak transcription	Ovary	ovary
5	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
6	chr1:224346600-224358200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:224346600-224363200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:224346600-224363200	Weak transcription	Fetal Stomach	stomach
9	chr1:224346600-224363400	Weak transcription	Right Ventricle	heart
10	chr1:224346600-224363400	Weak transcription	Spleen	Spleen
11	chr1:224348200-224358000	Weak transcription	Hela-S3	cervix
12	chr1:224348400-224358200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:224350000-224357800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:224350200-224358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:224355400-224359200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:224355600-224359000	Enhancers	Placenta	Placenta
17	chr1:224356000-224358600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:224356000-224358600	Enhancers	Fetal Thymus	thymus
19	chr1:224356000-224359000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:224356200-224359000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:224356200-224359000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:224356200-224359200	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:224356400-224358400	Enhancers	HepG2	liver
24	chr1:224356400-224358400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:224356400-224358600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:224356400-224358600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:224356400-224359000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:224356400-224359000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:224356400-224359000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:224356400-224359000	Enhancers	NHEK	skin
31	chr1:224356600-224358400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:224356600-224358400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:224356600-224358400	Enhancers	NH-A	brain
34	chr1:224356600-224358400	Enhancers	NHLF	lung
35	chr1:224356600-224358600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:224356600-224358600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr1:224356600-224358600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr1:224356600-224358600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:224356600-224358600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:224356600-224358600	Enhancers	Thymus	Thymus
41	chr1:224356800-224358600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr1:224356800-224359000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:224357000-224357800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:224357000-224357800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:224357000-224358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:224357000-224358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:224357000-224358200	Enhancers	A549	lung
48	chr1:224357000-224358200	Weak transcription	HMEC	breast
49	chr1:224357000-224358400	Weak transcription	Right Atrium	heart
50	chr1:224357000-224358600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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