Variant report

Variant	rs4923989
Chromosome Location	chr15:45020317-45020318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10163110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444818	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1137516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634059	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634063	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11639157	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12912870	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1630168	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1669833	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1690313	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16974543	1.00[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1720723	1.00[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1720724	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1869125	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901530	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1901538	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1993152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1993153	0.99[ASN][1000 genomes]
rs2084835	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2167595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468067	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470908	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2960206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3100140	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3100141	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3110677	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923990	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923991	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62024991	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62025968	0.94[EUR][1000 genomes]
rs62025969	0.91[EUR][1000 genomes]
rs6416439	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6416440	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493112	0.99[ASN][1000 genomes]
rs6493114	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493116	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493119	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493124	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493126	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493127	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6493128	0.94[EUR][1000 genomes]
rs7151	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165535	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs7168090	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172357	0.94[EUR][1000 genomes]
rs7172376	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7496437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7496559	0.87[EUR][1000 genomes]
rs7497862	0.83[ASN][1000 genomes]
rs8035787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038532	0.91[EUR][1000 genomes]
rs935885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs935888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs935889	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4923989	TRIM69	cis	lymphoblastoid	seeQTL
rs4923989	METT5D1	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45004600-45020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:45009400-45020600	Weak transcription	Brain Angular Gyrus	brain
3	chr15:45009400-45020600	Weak transcription	Pancreas	Pancrea
4	chr15:45009400-45020600	Weak transcription	Right Ventricle	heart
5	chr15:45009400-45020800	Weak transcription	Aorta	Aorta
6	chr15:45009600-45020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:45009600-45020800	Weak transcription	Fetal Brain Male	brain
8	chr15:45010200-45020600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:45010200-45020600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:45010200-45020600	Weak transcription	Fetal Kidney	kidney
11	chr15:45010600-45020600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:45010600-45020600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:45010800-45020600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:45010800-45020600	Weak transcription	Ovary	ovary
15	chr15:45011000-45020600	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:45011000-45020600	Weak transcription	Fetal Stomach	stomach
17	chr15:45011400-45020600	Weak transcription	Fetal Lung	lung
18	chr15:45011800-45020800	Weak transcription	Gastric	stomach
19	chr15:45015400-45021000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr15:45016000-45020600	Enhancers	Fetal Thymus	thymus
21	chr15:45016800-45021000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr15:45017000-45020400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr15:45017600-45020400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr15:45017600-45020400	Enhancers	Small Intestine	intestine
25	chr15:45017600-45020600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr15:45018000-45021000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:45018200-45020600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr15:45018200-45020600	Enhancers	Liver	Liver
29	chr15:45018200-45020600	Enhancers	Stomach Mucosa	stomach
30	chr15:45018200-45021000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr15:45018400-45020400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:45018400-45020400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:45018400-45020400	Enhancers	HMEC	breast
34	chr15:45018400-45020400	Enhancers	NH-A	brain
35	chr15:45018400-45020600	Enhancers	Fetal Intestine Large	intestine
36	chr15:45018400-45020600	Enhancers	Fetal Intestine Small	intestine
37	chr15:45018400-45020600	Enhancers	Fetal Muscle Leg	muscle
38	chr15:45018400-45020600	Enhancers	NHLF	lung
39	chr15:45018400-45020600	Enhancers	Osteobl	bone
40	chr15:45018400-45021000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:45018600-45020400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:45018600-45020600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:45018800-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:45019000-45020400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr15:45019000-45020400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:45019000-45020400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:45019000-45020400	Flanking Active TSS	GM12878-XiMat	blood
48	chr15:45019000-45020400	Enhancers	HUVEC	blood vessel
49	chr15:45019000-45020400	Enhancers	K562	blood
50	chr15:45019000-45020600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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