Variant report

Variant	rs2228528
Chromosome Location	chr10:50732280-50732281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF274	chr10:50731895-50732574	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:50729482..50733326-chr10:50734602..50739448,5	K562	blood:
2	chr10:50724821..50729589-chr10:50731335..50734731,5	K562	blood:
3	chr10:50731383..50733326-chr10:50736507..50739448,3	K562	blood:

Variant related genes	Relation type
PGBD3	TF binding region
ENSG00000243251	Chromatin interaction
ENSG00000225830	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1012553	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1012554	0.99[ASN][1000 genomes]
rs10776576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10776579	0.80[ASN][1000 genomes]
rs10776580	0.81[ASN][1000 genomes]
rs10857498	0.81[AMR][1000 genomes]
rs10857500	0.82[AMR][1000 genomes]
rs10857503	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857505	0.81[ASN][1000 genomes]
rs11101137	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs11101140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11101148	0.92[ASN][1000 genomes]
rs11101153	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11101154	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11527799	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11527805	0.85[CHB][hapmap]
rs11594945	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11815415	0.90[ASN][1000 genomes]
rs12161717	0.81[ASN][1000 genomes]
rs12161719	0.80[ASN][1000 genomes]
rs12217467	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12218455	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12218602	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12220085	0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs12220258	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12413113	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs17177703	0.81[ASN][1000 genomes]
rs17177717	0.82[CHB][hapmap]
rs17784189	0.81[ASN][1000 genomes]
rs1880679	0.81[ASN][1000 genomes]
rs1880680	0.81[ASN][1000 genomes]
rs1917799	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1924488	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2222638	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2228524	0.99[ASN][1000 genomes]
rs2281794	0.86[CHB][hapmap];0.82[AMR][1000 genomes]
rs2377901	0.80[ASN][1000 genomes]
rs28454254	0.82[AMR][1000 genomes]
rs2889771	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750745	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750748	0.86[CHB][hapmap];0.82[AMR][1000 genomes]
rs3750749	0.82[AMR][1000 genomes]
rs3763728	0.89[ASN][1000 genomes]
rs3793786	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3793788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4012459	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240507	0.93[ASN][1000 genomes]
rs4240508	0.95[ASN][1000 genomes]
rs4253009	0.93[ASN][1000 genomes]
rs4253013	0.86[CHB][hapmap];0.88[MEX][hapmap]
rs4253024	0.99[ASN][1000 genomes]
rs4253040	0.82[AMR][1000 genomes]
rs4253043	0.86[CHB][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs4253060	0.86[CHB][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs4253082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4253095	0.86[CHB][hapmap];0.82[AMR][1000 genomes]
rs4253138	0.81[AMR][1000 genomes]
rs4253145	0.81[AMR][1000 genomes]
rs4253226	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56002988	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57761316	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59219652	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61288726	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6537537	0.90[ASN][1000 genomes]
rs7080607	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7082895	0.93[ASN][1000 genomes]
rs7087700	0.95[ASN][1000 genomes]
rs7096755	0.89[ASN][1000 genomes]
rs7100059	0.81[ASN][1000 genomes]
rs73305562	0.82[AMR][1000 genomes]
rs7901433	0.90[ASN][1000 genomes]
rs7909342	0.82[AMR][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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised 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	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1051636	chr10:50675292-50732280	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv933981	chr10:50730049-50732868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2228528	PARG	cis	parietal	SCAN
rs2228528	ERCC6	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50707600-50735600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr10:50717200-50736200	Weak transcription	Colon Smooth Muscle	Colon
3	chr10:50717200-50746000	Weak transcription	Fetal Heart	heart
4	chr10:50717400-50737000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:50720400-50746200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:50721600-50734800	Weak transcription	A549	lung
7	chr10:50723000-50734400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:50723000-50741000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:50723200-50741000	Strong transcription	Primary T cells from cord blood	blood
10	chr10:50723200-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:50723200-50741000	Strong transcription	HMEC	breast
12	chr10:50723200-50741800	Strong transcription	Osteobl	bone
13	chr10:50723400-50739600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr10:50723400-50741000	Strong transcription	Fetal Intestine Large	intestine
15	chr10:50723400-50741000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr10:50723400-50741600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:50723400-50741600	Strong transcription	NHEK	skin
18	chr10:50723600-50741000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr10:50724400-50734800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr10:50725000-50746200	Weak transcription	Psoas Muscle	Psoas
21	chr10:50725400-50733000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr10:50726600-50734000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:50726800-50739600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:50727600-50734000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr10:50727800-50733400	Strong transcription	HUVEC	blood vessel
26	chr10:50727800-50741000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:50727800-50741000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:50727800-50741000	Strong transcription	Adipose Nuclei	Adipose
29	chr10:50727800-50741200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:50728000-50732600	Strong transcription	Thymus	Thymus
31	chr10:50728000-50734400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:50728200-50734200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr10:50728200-50741000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr10:50728200-50741400	Strong transcription	HSMM	muscle
35	chr10:50728400-50733000	Weak transcription	Fetal Brain Male	brain
36	chr10:50728400-50738600	Strong transcription	Fetal Thymus	thymus
37	chr10:50728400-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:50728400-50741000	Strong transcription	Placenta	Placenta
39	chr10:50728600-50732600	Enhancers	Brain Anterior Caudate	brain
40	chr10:50728600-50733000	Weak transcription	Fetal Kidney	kidney
41	chr10:50728600-50736800	Strong transcription	Fetal Lung	lung
42	chr10:50728600-50736800	Weak transcription	Gastric	stomach
43	chr10:50728600-50740600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:50728600-50741400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr10:50728800-50733000	Strong transcription	Primary B cells from cord blood	blood
46	chr10:50728800-50741000	Strong transcription	Dnd41	blood
47	chr10:50728800-50742000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:50729000-50745800	Weak transcription	Stomach Mucosa	stomach
49	chr10:50729200-50734400	Weak transcription	Brain Germinal Matrix	brain
50	chr10:50729200-50738600	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links