Variant report

Variant	rs17244452
Chromosome Location	chr20:25589119-25589120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25589103..25590623-chr3:128880296..128881849,2	K562	blood:
2	chr20:25589103..25590623-chr3:128879792..128881796,2	K562	blood:
3	chr20:25588843..25590699-chr20:25604414..25605941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261796	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction
ENSG00000240682	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10470065	0.88[AFR][1000 genomes]
rs11905437	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs16987806	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17857107	0.91[CEU][hapmap]
rs55652038	0.88[AFR][1000 genomes]
rs56184302	0.88[AFR][1000 genomes]
rs56243008	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6107049	0.87[EUR][1000 genomes]
rs6107071	0.88[AFR][1000 genomes]
rs6115177	1.00[CEU][hapmap]
rs6115178	1.00[CEU][hapmap]
rs6115193	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs6115202	0.86[YRI][hapmap]
rs6115208	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6115211	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6115223	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6115227	1.00[YRI][hapmap]
rs6115248	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6115256	0.94[AFR][1000 genomes]
rs7272126	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73102121	0.94[AFR][1000 genomes]
rs73111242	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73113144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17244452	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25573800-25590400	Weak transcription	Thymus	Thymus
2	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
3	chr20:25581600-25594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr20:25581800-25594000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:25582000-25593200	Weak transcription	Adipose Nuclei	Adipose
7	chr20:25582000-25594800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:25582000-25602800	Weak transcription	Osteobl	bone
9	chr20:25582200-25593000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:25583600-25594200	Weak transcription	Aorta	Aorta
11	chr20:25584400-25593800	Weak transcription	Liver	Liver
12	chr20:25585600-25595200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr20:25586000-25602600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr20:25586200-25593400	Weak transcription	Fetal Stomach	stomach
15	chr20:25586200-25602800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr20:25586400-25593800	Weak transcription	Fetal Thymus	thymus
17	chr20:25586800-25593400	Weak transcription	Ovary	ovary
18	chr20:25587000-25593600	Weak transcription	Left Ventricle	heart
19	chr20:25587000-25593800	Weak transcription	Fetal Muscle Leg	muscle
20	chr20:25587000-25594000	Weak transcription	HSMM	muscle
21	chr20:25587000-25603000	Weak transcription	HSMMtube	muscle
22	chr20:25587200-25589200	Weak transcription	HUVEC	blood vessel
23	chr20:25587200-25594400	Weak transcription	A549	lung
24	chr20:25587400-25600400	Weak transcription	K562	blood
25	chr20:25587600-25601400	Weak transcription	Pancreas	Pancrea
26	chr20:25588000-25589800	Enhancers	HepG2	liver
27	chr20:25588000-25595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:25588200-25593000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr20:25588200-25594400	Weak transcription	Primary T cells from cord blood	blood
30	chr20:25588400-25592200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr20:25588400-25597800	Strong transcription	Dnd41	blood
32	chr20:25588400-25599200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr20:25588600-25590400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr20:25588600-25596200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr20:25588600-25599400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr20:25588600-25599400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr20:25588600-25602800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr20:25588800-25595800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr20:25589000-25593000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links