Variant report

Variant	rs12904553
Chromosome Location	chr15:77845959-77845960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11854328	0.89[CHB][hapmap]
rs11857860	0.86[JPT][hapmap]
rs12900004	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.83[ASN][1000 genomes]
rs12901130	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12905285	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907746	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12913899	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886875	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs4886876	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4886877	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs60256831	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495240	0.89[JPT][hapmap]
rs7162637	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs907369	0.83[ASN][1000 genomes]
rs907372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12904553	CYP1A2	cis	cerebellum	SCAN
rs12904553	MPI	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77836200-77846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:77838600-77849800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:77838800-77849000	Weak transcription	Gastric	stomach
4	chr15:77839800-77846400	Weak transcription	Fetal Heart	heart
5	chr15:77840600-77848600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:77841400-77846600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:77841600-77846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:77841600-77846800	Weak transcription	Spleen	Spleen
9	chr15:77841600-77847000	Weak transcription	Fetal Brain Female	brain
10	chr15:77841600-77849600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:77842200-77850200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr15:77842800-77850400	Enhancers	Brain Hippocampus Middle	brain
13	chr15:77843400-77846400	Weak transcription	Fetal Stomach	stomach
14	chr15:77843600-77846200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:77843800-77846000	Bivalent Enhancer	HepG2	liver
16	chr15:77843800-77847400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:77844000-77846000	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:77844000-77846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:77844400-77846600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr15:77844400-77848400	Weak transcription	Fetal Intestine Small	intestine
21	chr15:77844400-77850200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:77844600-77850000	Enhancers	Brain Anterior Caudate	brain
23	chr15:77844800-77848200	Enhancers	Brain Angular Gyrus	brain
24	chr15:77844800-77849800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:77844800-77849800	Enhancers	Brain Substantia Nigra	brain
26	chr15:77845000-77849400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:77845200-77846200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:77845200-77846200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:77845200-77846200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:77845400-77846200	Enhancers	Fetal Brain Male	brain
31	chr15:77845400-77846600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:77845600-77847200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:77845800-77846000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:77845800-77846000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links