Variant report

Variant	rs2387976
Chromosome Location	chr20:25599560-25599561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25579638..25582269-chr20:25599435..25601779,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13040726	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]
rs16987764	1.00[CHB][hapmap]
rs1983974	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2387977	0.84[CEU][hapmap]
rs34485039	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs374701	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs3752273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs376742	1.00[ASW][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs404775	1.00[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs405822	1.00[YRI][hapmap]
rs409853	1.00[YRI][hapmap]
rs4423675	1.00[ASW][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs443009	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4815437	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6037158	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6050679	0.91[MEX][hapmap]
rs6076364	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6076366	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6076369	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6083891	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6107060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6107062	1.00[CHB][hapmap]
rs6107064	1.00[CHB][hapmap]
rs6115190	1.00[CHB][hapmap]
rs6115210	0.90[AFR][1000 genomes]
rs7268237	1.00[CHB][hapmap]
rs958075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2387976	PYGB	cis	cerebellum	SCAN
rs2387976	ABHD12	cis	lymphoblastoid	seeQTL
rs2387976	ABHD12	cis	cerebellum	SCAN
rs2387976	ABHD12	cis	Cerebellum	GTEx
rs2387976	ABHD12	cis	multi-tissue	Pritchard
rs2387976	NINL	cis	cerebellum	SCAN
rs2387976	ENTPD6	cis	cerebellum	SCAN
rs2387976	ABHD12	cis	uninvolved skin	skin_eQTL
rs2387976	ABHD12	cis	Brain Pons	GTEx
rs2387976	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs2387976	NINL	cis	parietal	SCAN
rs2387976	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs2387976	ABHD12	cis	Temporal Cortex	GTEx
rs2387976	ABHD12	cis	Frontal Cortex	GTEx
rs2387976	GINS1	cis	parietal	SCAN
rs2387976	NINL	cis	Thyroid	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
2	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:25582000-25602800	Weak transcription	Osteobl	bone
4	chr20:25586000-25602600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:25586200-25602800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr20:25587000-25603000	Weak transcription	HSMMtube	muscle
7	chr20:25587400-25600400	Weak transcription	K562	blood
8	chr20:25587600-25601400	Weak transcription	Pancreas	Pancrea
9	chr20:25588600-25602800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr20:25589200-25601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:25589200-25602600	Weak transcription	Right Ventricle	heart
12	chr20:25590800-25602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr20:25590800-25603200	Weak transcription	Fetal Intestine Large	intestine
14	chr20:25591000-25603600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr20:25591400-25602800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr20:25591600-25600200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr20:25591600-25602800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr20:25591600-25603000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr20:25591600-25603200	Weak transcription	Fetal Lung	lung
20	chr20:25592200-25602600	Weak transcription	Colon Smooth Muscle	Colon
21	chr20:25592200-25602600	Weak transcription	NHLF	lung
22	chr20:25592200-25602800	Weak transcription	Small Intestine	intestine
23	chr20:25592200-25602800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr20:25592200-25603200	Weak transcription	Brain Germinal Matrix	brain
25	chr20:25592600-25602800	Weak transcription	Esophagus	oesophagus
26	chr20:25592600-25603200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr20:25592800-25603200	Weak transcription	Fetal Kidney	kidney
28	chr20:25592800-25603200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr20:25593000-25602800	Weak transcription	NH-A	brain
30	chr20:25593200-25600400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:25593600-25602800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr20:25593800-25603000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:25594000-25602800	Weak transcription	Spleen	Spleen
34	chr20:25594000-25603200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr20:25594200-25600400	Weak transcription	Primary B cells from cord blood	blood
36	chr20:25594200-25602800	Weak transcription	Brain Angular Gyrus	brain
37	chr20:25594200-25602800	Weak transcription	Psoas Muscle	Psoas
38	chr20:25594200-25603200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr20:25594200-25603200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr20:25594200-25603200	Weak transcription	Fetal Intestine Small	intestine
41	chr20:25594200-25603200	Weak transcription	Ovary	ovary
42	chr20:25594200-25603400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr20:25595200-25603200	Weak transcription	Placenta	Placenta
44	chr20:25595600-25602800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr20:25595600-25602800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr20:25595800-25602800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr20:25595800-25603200	Weak transcription	Fetal Stomach	stomach
48	chr20:25596000-25602800	Weak transcription	Brain Anterior Caudate	brain
49	chr20:25596000-25602800	Weak transcription	Left Ventricle	heart
50	chr20:25596000-25603200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links