Variant report

Variant	rs2682920
Chromosome Location	chr15:77869917-77869918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77864365..77867025-chr15:77869640..77872108,2	MCF-7	breast:
2	chr15:77867409..77870567-chr15:77872173..77875130,4	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12593111	0.92[ASN][1000 genomes]
rs2460770	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2667766	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2667768	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2667769	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2667770	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2667771	0.88[ASN][1000 genomes]
rs2667772	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2667773	0.96[ASN][1000 genomes]
rs2667774	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2667776	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667777	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667778	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667779	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2667780	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682909	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2682911	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682912	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682913	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2682914	0.96[ASN][1000 genomes]
rs2682915	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682916	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682918	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682919	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682923	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682925	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682926	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28393270	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28612444	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35971869	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868297	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs868299	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907378	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907379	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907380	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907381	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907382	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907384	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs939486	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs939487	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs939491	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs939492	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939493	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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
5	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
6	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
7	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
8	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2682920	CYP1A2	cis	cerebellum	SCAN
rs2682920	MPI	cis	cerebellum	SCAN
rs2682920	UBE2Q2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77862200-77875000	Weak transcription	Left Ventricle	heart
2	chr15:77864000-77871400	Weak transcription	Spleen	Spleen
3	chr15:77868000-77870400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:77868000-77870400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:77868200-77871600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:77868400-77872000	Enhancers	Fetal Muscle Leg	muscle
7	chr15:77868400-77874400	Weak transcription	Fetal Intestine Small	intestine
8	chr15:77868400-77874600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:77868600-77871400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:77868600-77874600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:77868800-77871000	Enhancers	Fetal Muscle Trunk	muscle
12	chr15:77868800-77871400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:77869000-77871400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr15:77869000-77872000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:77869200-77871600	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:77869400-77870200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:77869400-77870200	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr15:77869400-77870200	Enhancers	HSMM	muscle
19	chr15:77869400-77870600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:77869400-77870600	Enhancers	Brain Angular Gyrus	brain
21	chr15:77869400-77870600	Enhancers	Right Ventricle	heart
22	chr15:77869400-77871200	Enhancers	Brain Anterior Caudate	brain
23	chr15:77869400-77871200	Enhancers	Brain Hippocampus Middle	brain
24	chr15:77869400-77871200	Enhancers	Brain Substantia Nigra	brain
25	chr15:77869400-77871600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:77869400-77871600	Enhancers	HSMMtube	muscle
27	chr15:77869400-77871800	Enhancers	Placenta	Placenta
28	chr15:77869600-77870000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:77869600-77870200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:77869600-77870200	Enhancers	Colon Smooth Muscle	Colon
31	chr15:77869600-77870400	Enhancers	Fetal Heart	heart
32	chr15:77869600-77870800	Enhancers	Fetal Stomach	stomach
33	chr15:77869800-77870200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:77869800-77870200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:77869800-77870200	Enhancers	Fetal Brain Female	brain
36	chr15:77869800-77870400	Enhancers	Fetal Brain Male	brain
37	chr15:77869800-77870800	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links