Variant report

Variant	rs544588
Chromosome Location	chr5:14227482-14227483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14143875..14146353-chr5:14226756..14228608,4	MCF-7	breast:
2	chr5:14219689..14221561-chr5:14226743..14228313,2	K562	blood:
3	chr5:14220578..14224492-chr5:14225553..14229108,5	MCF-7	breast:
4	chr5:14143211..14145385-chr5:14226496..14228720,2	K562	blood:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11133784	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11743665	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs12522960	0.80[ASN][1000 genomes]
rs149123	0.89[ASN][1000 genomes]
rs151899	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs151900	0.89[ASN][1000 genomes]
rs151924	0.80[ASN][1000 genomes]
rs164629	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs16903264	0.86[JPT][hapmap]
rs171592	0.80[ASN][1000 genomes]
rs245445	0.89[ASN][1000 genomes]
rs248899	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26114	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26136	0.82[ASN][1000 genomes]
rs26137	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26281	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs27463	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28014	0.85[TSI][hapmap]
rs30621	0.82[CEU][hapmap]
rs30631	0.82[CEU][hapmap]
rs32392	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32548	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32549	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33004	0.80[ASN][1000 genomes]
rs352112	0.81[ASN][1000 genomes]
rs354286	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[ASN][1000 genomes]
rs39617	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701604	0.81[ASN][1000 genomes]
rs506330	0.89[ASN][1000 genomes]
rs556928	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs58185757	0.88[ASN][1000 genomes]
rs706278	0.90[ASN][1000 genomes]
rs72744212	0.85[AFR][1000 genomes];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	nsv534466	chr5:13847044-14246208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv4724	chr5:14225543-14243167	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14217000-14234600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:14218400-14230000	Weak transcription	NHEK	skin
3	chr5:14219200-14228800	Enhancers	Fetal Thymus	thymus
4	chr5:14219800-14229400	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:14219800-14231000	Weak transcription	HMEC	breast
6	chr5:14219800-14231200	Weak transcription	Fetal Stomach	stomach
7	chr5:14220000-14229400	Weak transcription	Brain Angular Gyrus	brain
8	chr5:14220000-14230000	Weak transcription	Fetal Brain Female	brain
9	chr5:14220400-14229400	Weak transcription	Brain Germinal Matrix	brain
10	chr5:14221800-14230800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:14221800-14231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:14221800-14249600	Weak transcription	Colonic Mucosa	Colon
13	chr5:14222600-14228200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:14222600-14228400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:14223400-14229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:14223400-14230200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr5:14223600-14229600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:14223600-14230000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:14223800-14229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:14223800-14230400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:14223800-14237600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:14224000-14228000	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:14224000-14231400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:14224000-14237400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:14224000-14239600	Weak transcription	Primary B cells from cord blood	blood
26	chr5:14224600-14228000	Enhancers	A549	lung
27	chr5:14225000-14227600	Enhancers	Left Ventricle	heart
28	chr5:14225000-14228800	Enhancers	Right Ventricle	heart
29	chr5:14225000-14230000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:14225000-14237600	Genic enhancers	HSMM	muscle
31	chr5:14225200-14227800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr5:14225200-14228000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr5:14225400-14228600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr5:14225400-14228800	Enhancers	Placenta	Placenta
35	chr5:14225400-14230600	Enhancers	Ovary	ovary
36	chr5:14225600-14227600	Enhancers	Pancreas	Pancrea
37	chr5:14225600-14227600	Enhancers	Right Atrium	heart
38	chr5:14225600-14228600	Enhancers	Adipose Nuclei	Adipose
39	chr5:14225600-14228800	Enhancers	Fetal Muscle Leg	muscle
40	chr5:14226000-14227600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr5:14226000-14228000	Enhancers	Psoas Muscle	Psoas
42	chr5:14226000-14230800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr5:14226200-14228600	Weak transcription	GM12878-XiMat	blood
44	chr5:14226200-14228800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:14226200-14229600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:14226200-14231000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:14226200-14237800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:14226400-14227600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr5:14226400-14227800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr5:14226400-14230400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links