Variant report

Variant	rs2282774
Chromosome Location	chr4:2905652-2905653
allele	C/G
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	POLR2A	chr4:2905620-2905683	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:2905460-2905680	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2905536..2909706-chr4:2929255..2933631,5	MCF-7	breast:
3	chr4:2905184..2907605-chr4:2907928..2912349,4	MCF-7	breast:

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087274	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1012365	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263338	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1263339	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1263342	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263344	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263345	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1263347	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1263349	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1263359	0.95[CHB][hapmap]
rs1263360	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs12642795	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419045	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16843452	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs16843523	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2051560	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071695	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2097081	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2185885	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237004	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2239728	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282772	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282773	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285084	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301374	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2857866	0.83[EUR][1000 genomes]
rs3775068	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3796469	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4690000	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4690001	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4690065	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4961	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4963	0.88[CEU][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73082333	0.88[ASN][1000 genomes]
rs73189458	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs762847	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7654786	0.83[ASN][1000 genomes]
rs7664801	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv1007958	chr4:2904137-2914601	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:2880600-2915000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:2883600-2918600	Strong transcription	Fetal Stomach	stomach
6	chr4:2890400-2918000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:2893000-2907800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:2893000-2919400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:2893200-2907600	Strong transcription	Primary T cells from cord blood	blood
10	chr4:2893200-2907600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr4:2893200-2914000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:2893200-2918800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr4:2893200-2918800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr4:2893200-2919200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
16	chr4:2893400-2915800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:2893400-2918800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:2893400-2919000	Strong transcription	Fetal Muscle Leg	muscle
19	chr4:2893800-2909200	Strong transcription	Lung	lung
20	chr4:2893800-2918600	Strong transcription	Thymus	Thymus
21	chr4:2893800-2919000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr4:2894000-2923000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:2894400-2907600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:2894600-2907600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:2894800-2919800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:2895000-2907600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:2895000-2917800	Strong transcription	Dnd41	blood
28	chr4:2895200-2907800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:2895200-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:2895200-2919000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr4:2895400-2907800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:2895400-2908200	Strong transcription	HepG2	liver
33	chr4:2895400-2913000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:2895400-2915200	Strong transcription	Placenta	Placenta
35	chr4:2895400-2916200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:2895400-2919000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:2895600-2914000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:2895600-2914200	Strong transcription	GM12878-XiMat	blood
39	chr4:2895600-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:2895600-2918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:2895600-2919200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:2895600-2919200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:2895800-2909000	Strong transcription	Liver	Liver
44	chr4:2895800-2919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:2895800-2919200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:2895800-2919200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr4:2896400-2911800	Strong transcription	Left Ventricle	heart
48	chr4:2896400-2917000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:2896400-2918000	Strong transcription	HSMMtube	muscle
50	chr4:2896600-2911400	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links