Variant report

Variant	rs4672026
Chromosome Location	chr2:55392510-55392511
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55275064..55280479-chr2:55390367..55395295,9	MCF-7	breast:
2	chr2:55391168..55392772-chr2:55394267..55395800,2	MCF-7	breast:
3	chr2:55240567..55242175-chr2:55391984..55393906,2	K562	blood:
4	chr2:55274543..55277923-chr2:55387934..55394752,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10172326	0.92[CEU][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10197309	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11125556	0.80[ASN][1000 genomes]
rs1133181	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133182	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679663	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685292	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12470651	0.80[ASN][1000 genomes]
rs12616435	0.81[ASN][1000 genomes]
rs12621144	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12990898	0.80[ASN][1000 genomes]
rs13012766	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013134	0.92[CEU][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13019355	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13021215	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13023235	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13417057	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs14026	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1437391	0.83[CEU][hapmap]
rs2164714	0.91[CEU][hapmap];0.81[ASN][1000 genomes]
rs2576724	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2864818	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34054131	0.82[ASN][1000 genomes]
rs34564471	0.92[ASN][1000 genomes]
rs35026006	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35161040	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35890669	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762509	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3935223	0.96[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420737	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671241	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671242	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672024	0.92[ASN][1000 genomes]
rs4672025	0.84[ASN][1000 genomes]
rs4672027	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56095114	0.92[ASN][1000 genomes]
rs56339196	0.81[ASN][1000 genomes]
rs6545474	0.92[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545475	0.80[CEU][hapmap];0.86[ASN][1000 genomes]
rs6545478	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714830	0.92[CEU][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6715130	0.81[ASN][1000 genomes]
rs6759911	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7595134	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7608118	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672026	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
2	chr2:55384000-55392800	Weak transcription	HMEC	breast
3	chr2:55386000-55395000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
5	chr2:55387400-55393800	Weak transcription	Fetal Heart	heart
6	chr2:55387400-55395600	Enhancers	Lung	lung
7	chr2:55387600-55395000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55388000-55395200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:55388600-55393200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:55388600-55393400	Enhancers	NH-A	brain
11	chr2:55388800-55395000	Weak transcription	Left Ventricle	heart
12	chr2:55389000-55394800	Enhancers	Brain Cingulate Gyrus	brain
13	chr2:55389000-55394800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:55389200-55393200	Enhancers	HUVEC	blood vessel
15	chr2:55389200-55394000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:55389200-55394800	Enhancers	Brain Anterior Caudate	brain
17	chr2:55389200-55397400	Enhancers	NHLF	lung
18	chr2:55389400-55394800	Enhancers	Brain Hippocampus Middle	brain
19	chr2:55389400-55395200	Weak transcription	NHEK	skin
20	chr2:55389800-55394000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55389800-55394600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:55389800-55395000	Weak transcription	Brain Germinal Matrix	brain
23	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
24	chr2:55390000-55393000	Enhancers	Colon Smooth Muscle	Colon
25	chr2:55390000-55393400	Enhancers	Fetal Kidney	kidney
26	chr2:55390000-55393600	Enhancers	Osteobl	bone
27	chr2:55390000-55393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:55390000-55395600	Enhancers	Ovary	ovary
29	chr2:55390200-55392800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:55390200-55393000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55390200-55394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:55390200-55395200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:55390400-55392600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:55390400-55394000	Enhancers	Fetal Intestine Small	intestine
35	chr2:55390400-55394800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:55390400-55395000	Weak transcription	Fetal Thymus	thymus
37	chr2:55390400-55395200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:55390400-55395600	Enhancers	Right Atrium	heart
39	chr2:55390600-55392600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:55390600-55392800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:55390600-55393200	Enhancers	A549	lung
42	chr2:55390600-55393800	Enhancers	Hela-S3	cervix
43	chr2:55390600-55395800	Enhancers	K562	blood
44	chr2:55390800-55394600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:55391000-55392600	Enhancers	HSMMtube	muscle
46	chr2:55391000-55394800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:55391000-55395400	Weak transcription	Spleen	Spleen
48	chr2:55391000-55397000	Enhancers	Brain Angular Gyrus	brain
49	chr2:55391200-55392800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:55391200-55392800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links