Variant report

Variant	rs8028999
Chromosome Location	chr15:40849408-40849409
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	chr15:40848640..40851135-chr15:40883399..40886206,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10400825	0.90[EUR][1000 genomes]
rs10467972	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070284	0.85[EUR][1000 genomes]
rs11070285	0.80[JPT][hapmap]
rs11070286	0.80[JPT][hapmap]
rs11070292	0.91[CEU][hapmap]
rs11629680	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11632061	0.87[CHB][hapmap]
rs11632370	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs11637239	0.91[EUR][1000 genomes]
rs11638742	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs11852694	0.80[JPT][hapmap]
rs11854763	0.85[EUR][1000 genomes]
rs11854986	0.80[JPT][hapmap]
rs11855334	0.80[JPT][hapmap]
rs11856438	0.80[JPT][hapmap]
rs11858113	0.80[JPT][hapmap]
rs12438955	0.85[EUR][1000 genomes]
rs12440468	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592882	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594548	0.83[CHB][hapmap]
rs12595610	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12708401	0.85[EUR][1000 genomes]
rs12911738	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs12912058	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs12912339	0.85[EUR][1000 genomes]
rs12914743	0.80[JPT][hapmap]
rs12915109	0.82[EUR][1000 genomes]
rs12916082	0.82[EUR][1000 genomes]
rs16970851	0.80[JPT][hapmap]
rs17747351	1.00[CEU][hapmap]
rs1901775	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304580	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs2412531	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2412532	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2412534	0.88[CHB][hapmap]
rs2412541	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2412544	0.80[JPT][hapmap]
rs2619681	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs2924388	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2959536	0.83[CHB][hapmap]
rs3092978	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs35047458	0.80[JPT][hapmap]
rs3751653	0.80[JPT][hapmap]
rs4417527	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4420508	0.85[EUR][1000 genomes]
rs4439732	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923876	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4924478	0.80[JPT][hapmap]
rs4924481	0.83[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap]
rs4924484	0.84[EUR][1000 genomes]
rs4924487	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4924488	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4924491	0.81[EUR][1000 genomes]
rs4924500	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs55640412	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492957	0.85[EUR][1000 genomes]
rs6492958	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6582	0.83[CHB][hapmap]
rs66885559	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7161968	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7162319	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7162509	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164289	0.91[EUR][1000 genomes]
rs7167417	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7168873	0.81[EUR][1000 genomes]
rs7171260	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7171945	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172947	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7176974	0.85[EUR][1000 genomes]
rs7177192	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7178486	0.85[EUR][1000 genomes]
rs72733486	0.86[EUR][1000 genomes]
rs7494968	0.83[CHB][hapmap]
rs8026605	0.80[JPT][hapmap]
rs8029384	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8031057	0.83[EUR][1000 genomes]
rs8035775	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8037417	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8037804	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8040502	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8042729	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896795	0.88[CHB][hapmap];0.85[YRI][hapmap]
rs896796	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs936580	0.80[EUR][1000 genomes]
rs9806221	0.84[EUR][1000 genomes]

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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8028999	FAM82A2	cis	parietal	SCAN
rs8028999	RMDN3	cis	Muscle Skeletal	GTEx
rs8028999	ZFYVE19	cis	cerebellum	SCAN
rs8028999	RASGRP1	cis	parietal	SCAN
rs8028999	PLA2G4D	cis	parietal	SCAN
rs8028999	C15orf57	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
2	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
3	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40838000-40856400	Weak transcription	A549	lung
6	chr15:40838600-40852800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:40839200-40849600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:40839200-40850000	Strong transcription	Fetal Thymus	thymus
10	chr15:40839400-40849600	Strong transcription	HMEC	breast
11	chr15:40839400-40850000	Strong transcription	Fetal Intestine Large	intestine
12	chr15:40839600-40849800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
14	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:40840400-40850600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:40842000-40849800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:40842000-40849800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:40842000-40849800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
20	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
21	chr15:40843600-40849600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:40843600-40850000	Strong transcription	Osteobl	bone
23	chr15:40843800-40850000	Strong transcription	Placenta	Placenta
24	chr15:40843800-40856400	Weak transcription	HSMMtube	muscle
25	chr15:40845000-40849600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:40845000-40849600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:40845000-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:40845000-40849800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:40845200-40849600	Strong transcription	Primary T cells from cord blood	blood
30	chr15:40845200-40849600	Strong transcription	NHEK	skin
31	chr15:40845600-40850600	Genic enhancers	K562	blood
32	chr15:40845800-40849600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:40846000-40855600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:40846200-40850800	Weak transcription	Pancreas	Pancrea
35	chr15:40846200-40851000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:40846200-40855000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:40846200-40856200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:40846400-40853400	Weak transcription	Thymus	Thymus
39	chr15:40846600-40849800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:40846600-40849800	Strong transcription	Fetal Muscle Leg	muscle
41	chr15:40846600-40851200	Weak transcription	Fetal Stomach	stomach
42	chr15:40846600-40853800	Weak transcription	Spleen	Spleen
43	chr15:40846600-40855000	Weak transcription	Psoas Muscle	Psoas
44	chr15:40846600-40855800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:40846600-40856400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:40846600-40856400	Weak transcription	Right Atrium	heart
47	chr15:40846600-40856600	Weak transcription	Aorta	Aorta
48	chr15:40846600-40856600	Weak transcription	Gastric	stomach
49	chr15:40846800-40856000	Weak transcription	Stomach Mucosa	stomach
50	chr15:40847000-40851200	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links