Variant report

Variant	rs62109409
Chromosome Location	chr2:20128346-20128347
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20123825..20126159-chr2:20127978..20130172,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12474041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12479284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731661	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731667	0.82[ASN][1000 genomes]
rs55924660	0.82[ASN][1000 genomes]
rs62109396	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62109400	0.84[ASN][1000 genomes]
rs62109407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6734005	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs72779339	0.83[ASN][1000 genomes]
rs72779347	0.84[ASN][1000 genomes]
rs736952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587014	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20128800	Weak transcription	Liver	Liver
2	chr2:20102800-20128800	Weak transcription	Brain Germinal Matrix	brain
3	chr2:20102800-20129000	Weak transcription	Brain Anterior Caudate	brain
4	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
5	chr2:20105400-20129000	Weak transcription	Primary T cells from cord blood	blood
6	chr2:20105400-20130200	Weak transcription	Lung	lung
7	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
8	chr2:20112200-20128400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:20112200-20130000	Weak transcription	HSMMtube	muscle
10	chr2:20112400-20128400	Weak transcription	NHDF-Ad	bronchial
11	chr2:20112600-20128800	Weak transcription	Hela-S3	cervix
12	chr2:20114000-20129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:20116400-20128800	Weak transcription	A549	lung
15	chr2:20116800-20128600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:20117000-20129000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:20121600-20130600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:20121600-20135800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:20122800-20130600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:20123400-20135800	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:20124400-20130600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:20125200-20129000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:20125200-20129000	Weak transcription	HUVEC	blood vessel
26	chr2:20125200-20132800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:20125400-20132800	Weak transcription	Gastric	stomach
28	chr2:20126200-20130400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:20126200-20130600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:20126400-20137200	Weak transcription	Colonic Mucosa	Colon
31	chr2:20126600-20129000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:20126600-20129000	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr2:20126600-20129400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr2:20126600-20129400	ZNF genes & repeats	Fetal Lung	lung
35	chr2:20126600-20130400	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr2:20126600-20130600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
37	chr2:20126800-20128400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr2:20126800-20128400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:20126800-20129000	Strong transcription	Fetal Kidney	kidney
40	chr2:20126800-20129600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:20126800-20129800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr2:20126800-20130400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr2:20126800-20130600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr2:20126800-20131200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:20127000-20129400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:20127000-20129800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:20127000-20130400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr2:20127000-20130400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
49	chr2:20127200-20130000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:20127200-20130600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links