Variant report

Variant	rs2304717
Chromosome Location	chr15:74326557-74326558
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	chr15:74312798..74315530-chr15:74325452..74327125,2	K562	blood:

Variant related genes	Relation type
ENSG00000140464	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10162627	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052242	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1052246	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10851868	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11072458	0.85[CEU][hapmap]
rs11072463	0.83[MEX][hapmap]
rs11072464	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072465	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072466	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072467	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633520	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11636016	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11636065	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636150	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12592370	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901603	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12902857	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12904213	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908748	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912395	0.81[AMR][1000 genomes]
rs12917179	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550434	0.81[YRI][hapmap]
rs2277599	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2304715	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2304716	0.81[ASW][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs2304718	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784562	0.96[CEU][hapmap]
rs4886844	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886845	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886846	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs734854	0.83[MEX][hapmap]
rs743581	0.85[ASN][1000 genomes]
rs8027327	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8027447	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8027774	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028557	0.81[AMR][1000 genomes]
rs8039276	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8043489	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription 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	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv518316	chr15:74290993-74331083	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv469619	chr15:74291859-74466321	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv482362	chr15:74291859-74466321	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv457203	chr15:74308940-74347723	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv569971	chr15:74308940-74347723	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
10	nsv510666	chr15:74310738-74394745	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2304717	ADPGK	cis	parietal	SCAN
rs2304717	PML	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74288200-74331000	Weak transcription	Fetal Heart	heart
2	chr15:74289800-74331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:74292000-74329200	Weak transcription	Fetal Brain Male	brain
4	chr15:74302400-74331000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:74303600-74331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:74306400-74330600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:74311000-74330400	Strong transcription	GM12878-XiMat	blood
8	chr15:74312200-74328000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:74312800-74330600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:74313000-74338600	Strong transcription	Primary T cells from cord blood	blood
11	chr15:74313600-74330000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:74314200-74338200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:74314400-74330400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:74314600-74330200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:74314600-74330400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:74314600-74338000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:74314800-74330400	Strong transcription	NHEK	skin
18	chr15:74315800-74327600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:74316000-74330600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:74316200-74326600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:74316400-74340400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:74316800-74326600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:74317400-74327600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:74318400-74329000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:74318400-74329400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:74318400-74331000	Weak transcription	Hela-S3	cervix
27	chr15:74318400-74331000	Weak transcription	K562	blood
28	chr15:74318400-74340200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:74318400-74340400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:74318800-74330800	Strong transcription	Osteobl	bone
31	chr15:74319200-74329000	Strong transcription	NHLF	lung
32	chr15:74320200-74328800	Strong transcription	Fetal Stomach	stomach
33	chr15:74320400-74327000	Weak transcription	HepG2	liver
34	chr15:74321200-74329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:74321400-74330000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:74322800-74336600	Strong transcription	Primary B cells from cord blood	blood
37	chr15:74323400-74332400	Strong transcription	Thymus	Thymus
38	chr15:74323600-74328800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:74323600-74329000	Strong transcription	Fetal Intestine Small	intestine
40	chr15:74323600-74330600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:74323800-74328000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:74323800-74328200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr15:74323800-74329000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:74323800-74329400	Strong transcription	Fetal Intestine Large	intestine
45	chr15:74323800-74329800	Strong transcription	HSMM	muscle
46	chr15:74323800-74330400	Strong transcription	Dnd41	blood
47	chr15:74323800-74330800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:74323800-74330800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:74324000-74328800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr15:74324200-74328800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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