Variant report

Variant	rs55986999
Chromosome Location	chr2:153596247-153596248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153572899..153575591-chr2:153595593..153597723,2	MCF-7	breast:
2	chr2:153589125..153592910-chr2:153595125..153598674,4	K562	blood:
3	chr2:153594973..153596577-chr2:153598285..153600899,2	K562	blood:

Variant related genes	Relation type
ENSG00000196504	Chromatin interaction
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10178618	0.89[ASN][1000 genomes]
rs11679491	0.87[ASN][1000 genomes]
rs11883762	0.92[ASN][1000 genomes]
rs12052946	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13018870	0.89[ASN][1000 genomes]
rs1561267	0.92[ASN][1000 genomes]
rs16831451	0.82[ASN][1000 genomes]
rs16831529	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831728	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272535	0.89[ASN][1000 genomes]
rs2293680	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748941	0.89[ASN][1000 genomes]
rs3817620	0.92[ASN][1000 genomes]
rs3845678	0.85[ASN][1000 genomes]
rs4146903	0.89[ASN][1000 genomes]
rs4664119	0.89[ASN][1000 genomes]
rs6710417	0.92[ASN][1000 genomes]
rs6714218	0.89[ASN][1000 genomes]
rs72858735	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871192	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72872615	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746780	0.90[ASN][1000 genomes]
rs7592127	0.89[ASN][1000 genomes]
rs893328	0.92[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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1798142	chr2:153578113-153600123	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875293	chr2:153578900-153617420	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv834422	chr2:153589448-153743069	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:153575800-153611600	Weak transcription	Esophagus	oesophagus
3	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
4	chr2:153576000-153615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:153577200-153617600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:153577600-153617800	Weak transcription	NHLF	lung
7	chr2:153578600-153605800	Weak transcription	Fetal Heart	heart
8	chr2:153579600-153602000	Weak transcription	Fetal Brain Male	brain
9	chr2:153579800-153599800	Weak transcription	A549	lung
10	chr2:153582000-153610600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:153583000-153611600	Weak transcription	Lung	lung
12	chr2:153587400-153603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:153587400-153608800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:153587400-153610600	Weak transcription	Small Intestine	intestine
15	chr2:153587600-153599800	Weak transcription	Stomach Mucosa	stomach
16	chr2:153587600-153602000	Weak transcription	Hela-S3	cervix
17	chr2:153587600-153618000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:153587600-153621600	Weak transcription	NHEK	skin
19	chr2:153588000-153617800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:153588200-153618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:153588600-153619400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:153589400-153613600	Weak transcription	Brain Angular Gyrus	brain
23	chr2:153589600-153601600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:153590200-153616800	Weak transcription	Right Ventricle	heart
25	chr2:153590400-153620400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:153590800-153596800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:153591000-153597000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:153591000-153611800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:153591200-153596800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:153591400-153596400	Strong transcription	Primary T cells from cord blood	blood
31	chr2:153591400-153596400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:153591400-153596400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:153591400-153596800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:153591400-153597000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr2:153591400-153597000	Strong transcription	Fetal Thymus	thymus
36	chr2:153591600-153596800	Strong transcription	Placenta	Placenta
37	chr2:153592000-153597000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:153592200-153618800	Weak transcription	HSMMtube	muscle
39	chr2:153592400-153596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:153592600-153596800	Strong transcription	Fetal Intestine Large	intestine
41	chr2:153592800-153596400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:153592800-153596600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:153592800-153596600	Strong transcription	Adipose Nuclei	Adipose
44	chr2:153592800-153596600	Strong transcription	HepG2	liver
45	chr2:153592800-153596800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr2:153592800-153596800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:153592800-153596800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr2:153592800-153596800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:153592800-153597000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:153593000-153596600	Strong transcription	Placenta Amnion	Placenta Amnion

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