Variant report

Variant	rs2682925
Chromosome Location	chr15:77860910-77860911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:77860907-77861278	H1-hESC	embryonic stem cell:	n/a	chr15:77861133-77861146 chr15:77861134-77861144
2	EBF1	chr15:77860592-77860911	GM12878	blood:	n/a	n/a
3	EBF1	chr15:77860566-77860926	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000259420	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12593111	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2460770	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667766	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2667768	0.84[ASN][1000 genomes]
rs2667769	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2667770	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2667771	0.84[ASN][1000 genomes]
rs2667772	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2667773	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2667774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667776	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667777	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667778	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667779	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667780	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682911	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2682912	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2682913	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2682914	0.91[ASN][1000 genomes]
rs2682915	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682916	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682918	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2682919	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682920	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682923	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682926	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393270	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28612444	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35971869	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868297	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs868299	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs907378	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907379	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907380	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs907381	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907382	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907384	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs939486	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs939487	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs939491	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs939492	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs939493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	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
7	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
8	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
9	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
10	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77855600-77862600	Enhancers	Brain Cingulate Gyrus	brain
2	chr15:77857200-77862600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:77857400-77862000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:77858800-77861000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:77858800-77861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:77859000-77862400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:77859200-77862000	Enhancers	Brain Anterior Caudate	brain
8	chr15:77859200-77862200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr15:77859400-77862600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:77859600-77861400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:77859600-77862200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr15:77859800-77861000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:77859800-77861400	Enhancers	Fetal Brain Female	brain
14	chr15:77860000-77861400	Enhancers	Fetal Lung	lung
15	chr15:77860000-77861600	Enhancers	Fetal Muscle Trunk	muscle
16	chr15:77860000-77862600	Enhancers	Fetal Stomach	stomach
17	chr15:77860000-77862800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:77860200-77861000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:77860200-77861200	Flanking Active TSS	HepG2	liver
20	chr15:77860200-77861400	Enhancers	Brain Hippocampus Middle	brain
21	chr15:77860200-77862400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:77860200-77862400	Enhancers	Brain Angular Gyrus	brain
23	chr15:77860200-77862400	Enhancers	Brain Substantia Nigra	brain
24	chr15:77860400-77861200	Enhancers	Ovary	ovary
25	chr15:77860400-77861400	Enhancers	Stomach Mucosa	stomach
26	chr15:77860400-77861600	Enhancers	Placenta	Placenta
27	chr15:77860400-77862400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr15:77860600-77861400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:77860600-77861400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr15:77860600-77861400	Enhancers	Stomach Smooth Muscle	stomach
31	chr15:77860600-77861600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr15:77860600-77861600	Enhancers	Fetal Intestine Small	intestine
33	chr15:77860600-77862400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:77860600-77862400	Enhancers	Fetal Brain Male	brain
35	chr15:77860800-77861000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:77860800-77861000	Enhancers	Colonic Mucosa	Colon
37	chr15:77860800-77861000	Enhancers	Fetal Thymus	thymus
38	chr15:77860800-77861000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr15:77860800-77861200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:77860800-77861200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr15:77860800-77861400	Enhancers	Liver	Liver
42	chr15:77860800-77861400	Enhancers	Duodenum Mucosa	Duodenum
43	chr15:77860800-77861400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr15:77860800-77861400	Enhancers	Right Atrium	heart
45	chr15:77860800-77861600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:77860800-77861600	Enhancers	Fetal Intestine Large	intestine
47	chr15:77860800-77861600	Enhancers	Gastric	stomach
48	chr15:77860800-77862200	Weak transcription	Lung	lung
49	chr15:77860800-77862400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:77860800-77862400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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