Variant report

Variant	rs11948100
Chromosome Location	chr5:90184818-90184819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90183752..90186174-chr5:90676365..90680151,3	MCF-7	breast:
2	chr5:90181377..90185761-chr5:90673383..90677784,5	K562	blood:
3	chr5:90184114..90185772-chr5:90277640..90279396,2	K562	blood:
4	chr5:90180905..90184179-chr5:90184592..90187757,3	K562	blood:
5	chr5:90183905..90185761-chr5:90676284..90678383,2	K562	blood:
6	chr5:90184781..90186579-chr5:90679255..90681231,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10942614	0.85[ASN][1000 genomes]
rs10942615	0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10942616	0.95[ASN][1000 genomes]
rs10942617	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11956677	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12658466	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16869291	0.87[CEU][hapmap]
rs1818350	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1828175	0.87[CEU][hapmap]
rs36088173	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4362971	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4382198	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4916692	0.85[CEU][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs4916824	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916825	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916830	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56851353	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58258039	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58884460	0.85[ASN][1000 genomes]
rs61006221	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6861214	0.85[CEU][hapmap];0.82[ASN][1000 genomes]
rs6863794	0.87[CEU][hapmap]
rs6886778	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6889598	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6893164	0.85[CEU][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs73771110	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73771113	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73771115	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73771117	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73771118	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73771119	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7709355	0.85[CEU][hapmap]

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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv2754394	chr5:90181320-90225796	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 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	chr5:90163600-90194400	Weak transcription	Pancreas	Pancrea
2	chr5:90165400-90188800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:90168200-90186000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:90174600-90185600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:90179600-90190200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90179800-90191600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:90179800-90192000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:90180600-90186600	Enhancers	Hela-S3	cervix
9	chr5:90180800-90190200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:90181400-90185400	Enhancers	NHEK	skin
11	chr5:90183200-90188600	Weak transcription	Esophagus	oesophagus
12	chr5:90183200-90192200	Weak transcription	Gastric	stomach
13	chr5:90183400-90186200	Enhancers	Liver	Liver
14	chr5:90183800-90185200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:90183800-90185600	Weak transcription	Stomach Mucosa	stomach
16	chr5:90184000-90185200	Enhancers	HUVEC	blood vessel
17	chr5:90184000-90186800	Enhancers	HepG2	liver
18	chr5:90184200-90185000	Enhancers	NH-A	brain
19	chr5:90184200-90185400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:90184400-90185000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:90184400-90185000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:90184400-90185000	Enhancers	Ovary	ovary
23	chr5:90184400-90185000	Enhancers	K562	blood
24	chr5:90184400-90186600	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr5:90184600-90185000	Enhancers	Small Intestine	intestine
26	chr5:90184600-90185200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:90184600-90185200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:90184600-90185400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr5:90184600-90186200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr5:90184800-90185000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:90184800-90185000	Enhancers	A549	lung
32	chr5:90184800-90185400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr5:90184800-90186600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr5:90184800-90186600	Enhancers	Fetal Intestine Large	intestine
35	chr5:90184800-90186600	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links