Variant report

Variant	rs13040726
Chromosome Location	chr20:25559881-25559882
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25559789..25563161-chr20:25564263..25567245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs16987764	1.00[CHB][hapmap]
rs1983974	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2387976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2387977	0.88[CEU][hapmap]
rs34485039	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374701	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs3752273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376742	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs390123	0.89[ASN][1000 genomes]
rs400357	0.89[ASN][1000 genomes]
rs404775	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs405822	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs409853	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4423675	1.00[YRI][hapmap]
rs443009	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4815429	0.89[ASN][1000 genomes]
rs4815431	0.89[ASN][1000 genomes]
rs4815437	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037158	1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6050679	0.89[ASN][1000 genomes]
rs6076343	0.89[ASN][1000 genomes]
rs6076358	0.89[ASN][1000 genomes]
rs6076364	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076366	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076369	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083824	0.95[YRI][hapmap]
rs6083845	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs6083851	0.89[ASN][1000 genomes]
rs6083860	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6083891	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107062	1.00[CHB][hapmap]
rs6107064	1.00[CHB][hapmap]
rs6115188	0.89[ASN][1000 genomes]
rs6115190	1.00[CHB][hapmap]
rs6115210	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6138593	0.89[ASN][1000 genomes]
rs7268237	1.00[CHB][hapmap]
rs869358	0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs958075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13040726	ABHD12	cis	Temporal Cortex	GTEx
rs13040726	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs13040726	ABHD12	cis	uninvolved skin	skin_eQTL
rs13040726	NINL	cis	Thyroid	GTEx
rs13040726	ABHD12	cis	Frontal Cortex	GTEx
rs13040726	ABHD12	cis	multi-tissue	Pritchard
rs13040726	ABHD12	cis	Brain Pons	GTEx
rs13040726	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs13040726	ABHD12	cis	Cerebellum	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
2	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:25532600-25565000	Weak transcription	HSMMtube	muscle
4	chr20:25534800-25561400	Weak transcription	Right Atrium	heart
5	chr20:25535000-25560000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:25535000-25561400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr20:25535800-25565000	Weak transcription	Fetal Kidney	kidney
8	chr20:25544600-25565000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr20:25546400-25565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr20:25548800-25565200	Weak transcription	Esophagus	oesophagus
11	chr20:25549000-25560000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:25550600-25560000	Weak transcription	HSMM	muscle
13	chr20:25550600-25561200	Weak transcription	Gastric	stomach
14	chr20:25552000-25565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr20:25552200-25564800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr20:25555200-25561200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:25555200-25564800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:25555200-25565000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:25555200-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr20:25555400-25561200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr20:25555400-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr20:25555400-25565000	Weak transcription	Brain Anterior Caudate	brain
23	chr20:25555400-25565000	Weak transcription	NHLF	lung
24	chr20:25555600-25560200	Weak transcription	Dnd41	blood
25	chr20:25557000-25565000	Weak transcription	Thymus	Thymus
26	chr20:25557200-25560000	Weak transcription	Fetal Thymus	thymus
27	chr20:25558000-25560000	Weak transcription	Brain Germinal Matrix	brain
28	chr20:25558200-25561400	Weak transcription	Pancreas	Pancrea
29	chr20:25558200-25565200	Weak transcription	Spleen	Spleen
30	chr20:25558400-25560000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr20:25558800-25561200	Strong transcription	Fetal Brain Female	brain
32	chr20:25559000-25562000	Enhancers	Fetal Heart	heart
33	chr20:25559400-25560600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr20:25559400-25560800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr20:25559600-25560000	Enhancers	H9 Cell Line	embryonic stem cell
36	chr20:25559600-25560000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr20:25559600-25560200	Enhancers	Fetal Lung	lung
38	chr20:25559600-25560400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr20:25559600-25560400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr20:25559600-25560400	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr20:25559600-25560400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr20:25559600-25560400	Genic enhancers	Fetal Intestine Small	intestine
43	chr20:25559600-25560400	Flanking Active TSS	HepG2	liver
44	chr20:25559600-25560400	Enhancers	NH-A	brain
45	chr20:25559600-25560600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr20:25559600-25560600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25559600-25560600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr20:25559600-25560600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr20:25559600-25560600	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr20:25559600-25561000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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