Variant report

Variant	rs12903362
Chromosome Location	chr15:75780960-75780961
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10851882	0.91[EUR][1000 genomes]
rs11072544	0.82[EUR][1000 genomes]
rs11072552	0.82[EUR][1000 genomes]
rs11632813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637263	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12324230	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909709	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911512	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915221	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916256	0.90[EUR][1000 genomes]
rs28376842	0.81[EUR][1000 genomes]
rs4319732	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4408507	0.82[EUR][1000 genomes]
rs4430707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4526985	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886442	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886449	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886702	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886704	0.88[EUR][1000 genomes]
rs4886705	0.95[EUR][1000 genomes]
rs4886706	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886718	0.81[EUR][1000 genomes]
rs6495172	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495173	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495174	0.85[EUR][1000 genomes]
rs6495176	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495178	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495181	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163783	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164541	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165292	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165469	0.86[EUR][1000 genomes]
rs7170660	0.88[EUR][1000 genomes]
rs7173220	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175139	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7176989	0.91[EUR][1000 genomes]
rs73436868	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8043300	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9806241	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv904387	chr15:75706296-75806911	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	64 gene(s)	inside rSNPs	diseases
9	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv904388	chr15:75730182-75804543	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	nsv904389	chr15:75739824-75806911	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv827390	chr15:75766087-75795370	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12903362	MAN2C1	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75749000-75797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:75749200-75782000	Weak transcription	Right Atrium	heart
3	chr15:75761600-75785200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75762200-75798000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:75762400-75792000	Weak transcription	Esophagus	oesophagus
6	chr15:75762400-75797800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:75762400-75798000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:75763600-75785800	Weak transcription	Psoas Muscle	Psoas
9	chr15:75763800-75797800	Weak transcription	Brain Substantia Nigra	brain
10	chr15:75764200-75781600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:75765600-75797800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:75766800-75798000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:75767200-75784800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:75768200-75783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:75771400-75781600	Weak transcription	Brain Anterior Caudate	brain
16	chr15:75771400-75782400	Weak transcription	Aorta	Aorta
17	chr15:75772000-75797800	Weak transcription	NHEK	skin
18	chr15:75772200-75781600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:75772200-75781600	Weak transcription	K562	blood
20	chr15:75772200-75781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:75772200-75782200	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:75772200-75794200	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:75772400-75781600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:75772400-75797800	Weak transcription	Fetal Brain Male	brain
25	chr15:75772400-75797800	Weak transcription	Right Ventricle	heart
26	chr15:75772400-75797800	Weak transcription	Spleen	Spleen
27	chr15:75772400-75798000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:75772600-75785000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:75775200-75783400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:75775200-75787200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:75775200-75788000	Strong transcription	Dnd41	blood
32	chr15:75775200-75789600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:75775200-75789800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:75775200-75795400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:75775200-75795400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr15:75775400-75782800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:75775400-75784800	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:75775400-75795400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:75775600-75783000	Strong transcription	Liver	Liver
40	chr15:75775600-75788600	Strong transcription	Fetal Intestine Large	intestine
41	chr15:75775800-75798000	Weak transcription	Fetal Heart	heart
42	chr15:75776000-75782600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr15:75776000-75783400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:75776000-75785800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:75776000-75786800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:75776000-75788400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:75776000-75795400	Strong transcription	Fetal Stomach	stomach
48	chr15:75776200-75795400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:75776800-75781000	Weak transcription	Brain Germinal Matrix	brain
50	chr15:75776800-75781600	Weak transcription	Fetal Kidney	kidney

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