Variant report

Variant	rs57877880
Chromosome Location	chr2:178622903-178622904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178121343..178124034-chr2:178622244..178624898,2	K562	blood:
2	chr2:178128837..178131144-chr2:178621737..178623732,2	K562	blood:
3	chr2:178614142..178617008-chr2:178620652..178623296,2	MCF-7	breast:
4	chr2:178620484..178623470-chr2:178626460..178628265,2	K562	blood:
5	chr2:178593275..178595968-chr2:178621315..178623404,2	K562	blood:

Variant related genes	Relation type
ENSG00000222043	Chromatin interaction
ENSG00000116044	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10497488	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497489	0.92[ASN][1000 genomes]
rs10930806	0.92[ASN][1000 genomes]
rs13031632	0.92[ASN][1000 genomes]
rs1344925	0.92[ASN][1000 genomes]
rs1370655	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1438041	0.84[AMR][1000 genomes]
rs16865764	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16865769	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34952652	0.92[ASN][1000 genomes]
rs3770028	0.92[ASN][1000 genomes]
rs3770043	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821007	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57242051	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57427125	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58408943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59657949	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60748325	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61334857	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61551597	0.84[AMR][1000 genomes]
rs62183005	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62183040	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62183042	0.84[AMR][1000 genomes]
rs62183043	0.84[AMR][1000 genomes]
rs6704720	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6731237	0.84[AMR][1000 genomes]
rs73030327	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030354	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934798	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178610600-178628200	Weak transcription	Pancreas	Pancrea
2	chr2:178614800-178624000	Enhancers	Fetal Muscle Leg	muscle
3	chr2:178617800-178624000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:178617800-178624000	Enhancers	Fetal Lung	lung
5	chr2:178618200-178623600	Enhancers	Fetal Stomach	stomach
6	chr2:178618400-178623200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:178618400-178628200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:178619200-178623200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:178619400-178623200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:178619400-178628400	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:178619600-178623000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:178619600-178623200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:178619600-178623200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:178619600-178623200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:178619600-178623200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:178619600-178623200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:178619600-178628200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:178619600-178628200	Weak transcription	Psoas Muscle	Psoas
19	chr2:178619600-178628200	Weak transcription	Right Atrium	heart
20	chr2:178619800-178623200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:178619800-178623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:178619800-178623200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:178620000-178623200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:178620000-178623200	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:178620200-178623200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:178620400-178623200	Weak transcription	Left Ventricle	heart
27	chr2:178620400-178623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:178620600-178628200	Weak transcription	Placenta	Placenta
29	chr2:178620800-178623400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:178621000-178623200	Weak transcription	Fetal Heart	heart
31	chr2:178621400-178624200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:178622200-178623200	Weak transcription	Ovary	ovary
33	chr2:178622400-178623200	Weak transcription	Fetal Kidney	kidney
34	chr2:178622400-178623600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:178622400-178625000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links