Variant report

Variant	rs2544779
Chromosome Location	chr5:127212887-127212888
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:127211793..127217903-chr5:127417278..127420388,8	MCF-7	breast:
2	chr5:127154107..127155724-chr5:127212443..127214983,2	MCF-7	breast:
3	chr5:127212385..127215145-chr5:127219355..127222619,3	MCF-7	breast:
4	chr5:127208944..127216752-chr5:127415805..127421659,21	MCF-7	breast:
5	chr5:127211016..127213453-chr5:127292897..127295874,2	MCF-7	breast:
6	chr5:127210281..127212908-chr5:127422377..127423931,2	MCF-7	breast:
7	chr5:127210963..127213061-chr5:127280494..127282424,2	MCF-7	breast:
8	chr5:127212523..127214164-chr5:127301948..127304809,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10042555	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058856	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs111941	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs111942	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs122730	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs122731	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs122734	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332194	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332385	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332386	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332552	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421748	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421749	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421750	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1421751	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151853	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151855	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151856	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151858	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151859	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520247	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs173444	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187381	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193495	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2006195	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2108653	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409033	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245156	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs245158	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs245160	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs245167	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245172	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245174	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245175	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245221	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs245237	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2544780	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681512	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764766	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127194200-127213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:127207000-127213600	Weak transcription	Gastric	stomach
3	chr5:127207000-127213800	Weak transcription	Left Ventricle	heart
4	chr5:127207800-127220800	Weak transcription	Brain Angular Gyrus	brain
5	chr5:127209600-127213600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:127211400-127214000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:127211600-127216800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:127211600-127220600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:127211800-127213000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr5:127211800-127213200	Weak transcription	HepG2	liver
11	chr5:127211800-127213600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:127211800-127213600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:127211800-127213600	Weak transcription	Fetal Stomach	stomach
14	chr5:127211800-127213800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:127211800-127213800	Weak transcription	HUVEC	blood vessel
16	chr5:127211800-127214000	Enhancers	Duodenum Mucosa	Duodenum
17	chr5:127211800-127214400	Enhancers	A549	lung
18	chr5:127212000-127213200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:127212000-127214400	Enhancers	Stomach Mucosa	stomach
20	chr5:127212200-127219600	Weak transcription	Small Intestine	intestine
21	chr5:127212400-127213000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:127212400-127213400	Weak transcription	GM12878-XiMat	blood
23	chr5:127212400-127213600	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:127212400-127213600	Weak transcription	Brain Substantia Nigra	brain
25	chr5:127212400-127217200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:127212400-127217200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:127212400-127220200	Weak transcription	Psoas Muscle	Psoas
28	chr5:127212400-127220800	Weak transcription	Fetal Lung	lung
29	chr5:127212600-127213000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:127212600-127213000	Weak transcription	Fetal Intestine Large	intestine
31	chr5:127212600-127213000	Weak transcription	Fetal Intestine Small	intestine
32	chr5:127212600-127213000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:127212600-127213400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:127212600-127213600	Weak transcription	Brain Anterior Caudate	brain
35	chr5:127212600-127213600	Weak transcription	HMEC	breast
36	chr5:127212600-127213800	Weak transcription	NHLF	lung
37	chr5:127212600-127214000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:127212600-127218400	Weak transcription	Fetal Kidney	kidney
39	chr5:127212800-127213200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links