Variant report

Variant	rs6510528
Chromosome Location	chr19:36684666-36684667
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10416729	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10418925	0.86[CHB][hapmap]
rs11084857	0.82[CHB][hapmap]
rs1129375	0.86[CHB][hapmap]
rs1129376	0.86[CHB][hapmap];0.83[TSI][hapmap]
rs11673662	0.85[ASN][1000 genomes]
rs11882601	0.85[CHB][hapmap]
rs12460237	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12608941	0.96[ASN][1000 genomes]
rs12609058	0.86[CHB][hapmap]
rs17639740	0.86[CHB][hapmap]
rs2287897	0.80[LWK][hapmap];0.80[YRI][hapmap]
rs2432040	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2432044	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2432046	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432048	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432050	0.82[ASN][1000 genomes]
rs2432053	0.86[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs2432055	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2438515	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438516	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2910681	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2918324	0.92[EUR][1000 genomes]
rs2918325	0.86[CHB][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs2918376	0.86[ASN][1000 genomes]
rs2918377	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2918381	0.85[ASN][1000 genomes]
rs2918384	0.86[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs2967490	0.86[CHB][hapmap];0.83[TSI][hapmap]
rs2967491	0.86[CHB][hapmap];0.83[TSI][hapmap]
rs2972528	0.91[EUR][1000 genomes]
rs2972532	0.92[EUR][1000 genomes]
rs2972533	0.86[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs2972535	0.85[ASN][1000 genomes]
rs2972540	0.80[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs2972543	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972630	0.86[CHB][hapmap]
rs2972631	0.86[CHB][hapmap]
rs2972643	0.86[CHB][hapmap]
rs2972654	0.86[CHB][hapmap]
rs2972655	0.86[CHB][hapmap]
rs34912665	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4293497	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4315447	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57614488	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60277419	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8107260	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107616	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv579425	chr19:36643695-36685753	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6510528	BCAM	cis	parietal	SCAN
rs6510528	ACTN4	cis	cerebellum	SCAN
rs6510528	ZNF527	cis	cerebellum	SCAN
rs6510528	ZNF565	trans	parietal	SCAN
rs6510528	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs6510528	ZFP82	cis	lymphoblastoid	seeQTL
rs6510528	GMFG	cis	cerebellum	SCAN
rs6510528	PSMC4	cis	parietal	SCAN
rs6510528	ZNF781	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36661800-36686800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:36662000-36684800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:36669200-36685000	Weak transcription	Stomach Mucosa	stomach
4	chr19:36669600-36704800	Weak transcription	Psoas Muscle	Psoas
5	chr19:36673800-36704800	Weak transcription	Fetal Kidney	kidney
6	chr19:36674000-36685200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:36674000-36704800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:36674200-36685000	Weak transcription	Fetal Thymus	thymus
9	chr19:36674200-36685600	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:36674200-36687200	Weak transcription	GM12878-XiMat	blood
11	chr19:36674400-36684800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:36674400-36684800	Weak transcription	Right Ventricle	heart
13	chr19:36674400-36685200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:36674400-36685200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:36674400-36690000	Weak transcription	NHDF-Ad	bronchial
16	chr19:36674400-36704600	Weak transcription	Fetal Brain Male	brain
17	chr19:36674600-36684800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr19:36674600-36684800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:36674600-36684800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:36674600-36684800	Weak transcription	Thymus	Thymus
21	chr19:36674600-36684800	Weak transcription	Dnd41	blood
22	chr19:36674600-36684800	Weak transcription	Osteobl	bone
23	chr19:36674600-36685000	Weak transcription	Primary B cells from cord blood	blood
24	chr19:36674600-36685000	Weak transcription	Esophagus	oesophagus
25	chr19:36674600-36685000	Weak transcription	Fetal Lung	lung
26	chr19:36674600-36685000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:36674600-36685000	Weak transcription	HSMM	muscle
28	chr19:36674600-36685200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:36674600-36685200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:36674600-36685600	Weak transcription	Colonic Mucosa	Colon
31	chr19:36674600-36685600	Weak transcription	HepG2	liver
32	chr19:36674600-36687200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:36674600-36687200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:36674600-36687400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:36674600-36687800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:36674600-36704600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:36674600-36704600	Weak transcription	HMEC	breast
38	chr19:36674600-36704600	Weak transcription	NH-A	brain
39	chr19:36674600-36704600	Weak transcription	NHEK	skin
40	chr19:36674600-36704800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:36674800-36684800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:36674800-36694400	Weak transcription	Fetal Heart	heart
43	chr19:36675000-36684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:36678000-36684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:36682600-36686000	Strong transcription	Lung	lung
46	chr19:36682600-36686200	Strong transcription	Liver	Liver
47	chr19:36682600-36686200	Strong transcription	Brain Angular Gyrus	brain
48	chr19:36682600-36687200	Weak transcription	Hela-S3	cervix
49	chr19:36682600-36705000	Weak transcription	Small Intestine	intestine
50	chr19:36682800-36685000	Weak transcription	Primary monocytes fromperipheralblood	blood

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