Variant report

Variant	rs2855777
Chromosome Location	chr4:55554155-55554156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11726190	0.84[CEU][hapmap]
rs11946333	0.89[YRI][hapmap]
rs17240054	0.89[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2237017	0.83[EUR][1000 genomes]
rs2237019	0.87[TSI][hapmap]
rs2237020	0.92[EUR][1000 genomes]
rs2237021	0.93[EUR][1000 genomes]
rs2237023	0.87[TSI][hapmap]
rs2282775	0.94[ASW][hapmap];0.81[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703461	0.89[TSI][hapmap]
rs2703488	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729669	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020821	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3020825	0.81[GIH][hapmap];0.89[TSI][hapmap]
rs3020826	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3111791	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3111795	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3111800	0.87[TSI][hapmap]
rs3134884	0.93[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34332764	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3796772	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56295037	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1009516	chr4:55548449-55560839	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55545600-55575800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:55545800-55562000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:55546800-55558000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:55548000-55561600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:55549000-55555200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:55549200-55559200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:55551000-55554400	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:55551000-55554400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:55551200-55554200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:55551400-55554200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:55551800-55561800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:55552000-55556000	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:55552200-55554200	Weak transcription	Brain Anterior Caudate	brain
14	chr4:55552200-55555600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:55553400-55555600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr4:55553600-55554400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:55553600-55554800	Enhancers	Osteobl	bone
18	chr4:55553600-55555000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:55553600-55555000	Enhancers	Primary T cells from cord blood	blood
20	chr4:55553600-55555200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:55553600-55555200	Enhancers	Fetal Thymus	thymus
22	chr4:55553800-55554400	Enhancers	Duodenum Mucosa	Duodenum
23	chr4:55553800-55554600	Enhancers	NH-A	brain
24	chr4:55553800-55554800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:55553800-55555000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:55553800-55555200	Enhancers	GM12878-XiMat	blood
27	chr4:55554000-55554200	Enhancers	Brain Hippocampus Middle	brain
28	chr4:55554000-55554400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr4:55554000-55554400	Enhancers	NHDF-Ad	bronchial
30	chr4:55554000-55554600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:55554000-55554600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:55554000-55554600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr4:55554000-55556000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links