Variant report

Variant	rs4520411
Chromosome Location	chr1:154523215-154523216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:154523114-154523480	GM12878	blood:	n/a	chr1:154523267-154523278
2	POLR2A	chr1:154523195-154523450	K562	blood:	n/a	n/a
3	BHLHE40	chr1:154523193-154523391	GM12878	blood:	n/a	n/a
4	EBF1	chr1:154523141-154523422	GM12878	blood:	n/a	chr1:154523267-154523278
5	POLR2A	chr1:154522694-154523550	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:154523145-154523450	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:154522634-154523246	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154457195..154459578-chr1:154521193..154523267,2	MCF-7	breast:
2	chr1:154450895..154452551-chr1:154521385..154523555,2	K562	blood:
3	chr1:154450895..154452428-chr1:154521385..154523605,2	K562	blood:

Variant related genes	Relation type
UBE2Q1-AS1	TF binding region
ENSG00000273110	Chromatin interaction
ENSG00000169291	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11265605	1.00[EUR][1000 genomes]
rs11265630	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194591	1.00[EUR][1000 genomes]
rs1817688	1.00[EUR][1000 genomes]
rs2340487	1.00[EUR][1000 genomes]
rs4078519	1.00[EUR][1000 genomes]
rs4240873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4393148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845369	1.00[EUR][1000 genomes]
rs4845632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845646	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6427694	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6683078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6684225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685108	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7515974	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7530737	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537595	1.00[EUR][1000 genomes]
rs7556118	1.00[EUR][1000 genomes]
rs9659545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9804125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154513600-154528400	Weak transcription	Right Atrium	heart
2	chr1:154517600-154523600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154518000-154526000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:154520000-154528200	Strong transcription	Placenta	Placenta
5	chr1:154520400-154523400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:154520600-154528400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:154520600-154528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:154520600-154528800	Strong transcription	Primary T cells from cord blood	blood
9	chr1:154520800-154528400	Strong transcription	Adipose Nuclei	Adipose
10	chr1:154520800-154528400	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr1:154520800-154528600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:154520800-154528800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:154521000-154528200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:154521000-154528200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:154521000-154528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:154521000-154528600	Strong transcription	Fetal Thymus	thymus
17	chr1:154521200-154523600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:154521200-154523600	Genic enhancers	Dnd41	blood
19	chr1:154521200-154525000	Strong transcription	HMEC	breast
20	chr1:154521200-154525200	Strong transcription	Psoas Muscle	Psoas
21	chr1:154521200-154525200	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:154521200-154525400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:154521200-154525800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:154521200-154526000	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:154521200-154526200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:154521200-154526200	Strong transcription	NHEK	skin
27	chr1:154521200-154527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:154521200-154528200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr1:154521200-154528200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:154521200-154528400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:154521200-154528400	Strong transcription	Primary B cells from cord blood	blood
32	chr1:154521200-154528400	Strong transcription	Brain Anterior Caudate	brain
33	chr1:154521200-154528400	Strong transcription	Brain Hippocampus Middle	brain
34	chr1:154521200-154528400	Strong transcription	HUVEC	blood vessel
35	chr1:154521200-154528400	Strong transcription	NH-A	brain
36	chr1:154521200-154528600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:154521200-154528600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:154521200-154528600	Strong transcription	HSMM	muscle
39	chr1:154521200-154528800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:154521200-154528800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:154521200-154528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:154521400-154524200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:154521400-154524600	Genic enhancers	Liver	Liver
44	chr1:154521400-154525200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:154521400-154525400	Strong transcription	Colon Smooth Muscle	Colon
46	chr1:154521400-154525600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:154521400-154525800	Strong transcription	Fetal Stomach	stomach
48	chr1:154521400-154527800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:154521400-154528000	Strong transcription	Brain Substantia Nigra	brain
50	chr1:154521400-154528200	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links