Variant report

Variant	rs62093903
Chromosome Location	chr18:29521176-29521177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29517111..29520943-chr18:29521139..29523956,5	MCF-7	breast:
2	chr18:29483369..29487458-chr18:29519948..29522209,3	K562	blood:
3	chr18:29485958..29488048-chr18:29520164..29521790,2	K562	blood:
4	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
5	chr18:29494660..29496304-chr18:29519916..29522258,2	K562	blood:
6	chr18:29520544..29523172-chr18:33708356..33710539,2	K562	blood:

Variant related genes	Relation type
ENSG00000134759	Chromatin interaction
ENSG00000222320	Chromatin interaction
ENSG00000141424	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000134758	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11081717	0.83[ASN][1000 genomes]
rs11081718	0.84[ASN][1000 genomes]
rs11081719	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11081720	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11081722	0.91[ASN][1000 genomes]
rs11081723	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11081724	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11081729	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659244	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11660557	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11661525	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11662697	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11665424	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11877256	0.93[ASN][1000 genomes]
rs12604691	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12605636	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12606354	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12606379	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12606882	0.93[ASN][1000 genomes]
rs12606962	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12607786	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12608051	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17741796	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17741967	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17742014	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17742105	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17804129	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276144	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291239	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28654480	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34180462	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35275842	0.93[ASN][1000 genomes]
rs3737373	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3737374	0.87[ASN][1000 genomes]
rs3810001	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3925536	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4539674	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4545895	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55706254	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56303347	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58098304	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62093860	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62093864	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62093866	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62093867	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62093868	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62093869	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62093873	0.93[ASN][1000 genomes]
rs62093900	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62093901	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62095507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62095508	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62095509	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62095510	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62095543	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62095544	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62095545	0.87[ASN][1000 genomes]
rs62095546	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62095547	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62095548	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6506947	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7226615	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7226713	0.93[ASN][1000 genomes]
rs7228817	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7233234	0.90[ASN][1000 genomes]
rs7234341	0.94[ASN][1000 genomes]
rs7234798	0.91[ASN][1000 genomes]
rs7237879	0.89[ASN][1000 genomes]
rs7239629	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72930222	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9635917	0.93[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	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29432600-29521400	Weak transcription	Stomach Mucosa	stomach
2	chr18:29478600-29522000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:29482400-29522000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:29482600-29521600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr18:29482800-29521600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr18:29493000-29521600	Weak transcription	Aorta	Aorta
7	chr18:29493400-29521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:29496600-29521400	Weak transcription	NHEK	skin
9	chr18:29500600-29521400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:29505200-29521800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr18:29506800-29521600	Weak transcription	A549	lung
12	chr18:29509600-29522000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr18:29509600-29522000	Weak transcription	Lung	lung
14	chr18:29510200-29521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr18:29511200-29521600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr18:29511400-29521200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr18:29511600-29521400	Weak transcription	NHLF	lung
18	chr18:29511800-29521400	Weak transcription	Fetal Kidney	kidney
19	chr18:29511800-29521400	Weak transcription	HSMM	muscle
20	chr18:29511800-29521400	Weak transcription	NHDF-Ad	bronchial
21	chr18:29512200-29521600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr18:29512200-29521600	Weak transcription	Brain Angular Gyrus	brain
23	chr18:29512200-29521600	Weak transcription	Brain Anterior Caudate	brain
24	chr18:29512400-29522000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr18:29512800-29521400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr18:29513800-29521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr18:29516400-29521200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr18:29516400-29521400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr18:29516400-29521400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr18:29516400-29521600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:29516600-29521200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr18:29516800-29521200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:29516800-29522000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:29516800-29522000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr18:29517400-29521200	Weak transcription	Fetal Intestine Large	intestine
36	chr18:29517400-29521400	Weak transcription	Thymus	Thymus
37	chr18:29517600-29521400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr18:29518000-29521600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:29518400-29521400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr18:29518400-29521600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr18:29518600-29521200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:29518600-29521400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:29518600-29521400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:29518600-29521600	Enhancers	Fetal Brain Male	brain
45	chr18:29518600-29521800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr18:29518600-29521800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr18:29519200-29521200	Enhancers	HepG2	liver
48	chr18:29519400-29521400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr18:29519400-29521400	Enhancers	Pancreas	Pancrea
50	chr18:29519400-29521600	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links