Variant report

Variant	rs12439323
Chromosome Location	chr15:51262790-51262791
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11070815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631037	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11633226	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441319	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs3759808	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775912	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];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775914	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170736	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs72742362	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742383	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72744339	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9806270	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
8	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
9	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12439323	GATM	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
3	chr15:51235200-51263800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:51243800-51283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:51250400-51264800	Weak transcription	NHEK	skin
6	chr15:51252200-51263400	Weak transcription	NHLF	lung
7	chr15:51252400-51283800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:51253400-51265600	Weak transcription	HMEC	breast
9	chr15:51255800-51263200	Weak transcription	HUVEC	blood vessel
10	chr15:51257200-51262800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:51257600-51264800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:51257600-51264800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:51257600-51272800	Weak transcription	Pancreas	Pancrea
14	chr15:51257800-51262800	Weak transcription	Right Ventricle	heart
15	chr15:51257800-51263000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:51257800-51264600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:51258000-51262800	Weak transcription	HSMMtube	muscle
18	chr15:51258000-51263200	Weak transcription	Small Intestine	intestine
19	chr15:51258200-51262800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:51259400-51264000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:51259400-51264400	Strong transcription	Osteobl	bone
22	chr15:51259600-51263000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:51259600-51263600	Strong transcription	Ovary	ovary
24	chr15:51259600-51265200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr15:51259800-51267000	Strong transcription	Placenta	Placenta
26	chr15:51260400-51262800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:51260400-51267000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:51260600-51263600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:51260600-51268400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:51260800-51262800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:51260800-51262800	Strong transcription	Liver	Liver
32	chr15:51260800-51262800	Strong transcription	Brain Cingulate Gyrus	brain
33	chr15:51260800-51263200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:51260800-51263200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:51260800-51263600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:51260800-51264800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:51260800-51265800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr15:51260800-51268000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:51261000-51263400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:51261000-51265200	Strong transcription	Fetal Thymus	thymus
41	chr15:51261000-51269200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:51261200-51263000	Strong transcription	Fetal Kidney	kidney
43	chr15:51261200-51263000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:51261200-51263200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:51261200-51263400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:51261200-51263600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:51261200-51265400	ZNF genes & repeats	Fetal Brain Female	brain
48	chr15:51261200-51265400	Strong transcription	HSMM	muscle
49	chr15:51261200-51268200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr15:51261400-51263000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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