Variant report

Variant	rs55820245
Chromosome Location	chr2:54656255-54656256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54655292..54657691-chr2:54665507..54667789,2	K562	blood:
2	chr2:54641076..54644026-chr2:54655042..54656989,2	MCF-7	breast:
3	chr2:54643458..54646065-chr2:54654925..54657568,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10197675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200373	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13410583	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13422533	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17045872	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17045876	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045879	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17045894	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5027315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55988726	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57310962	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58805636	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59072058	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59850878	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72911198	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911200	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587404	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54639400-54657200	Weak transcription	Brain Anterior Caudate	brain
2	chr2:54648000-54657000	Weak transcription	Lung	lung
3	chr2:54652200-54656800	Weak transcription	Left Ventricle	heart
4	chr2:54654000-54663200	Enhancers	Fetal Muscle Leg	muscle
5	chr2:54654000-54664200	Enhancers	Adipose Nuclei	Adipose
6	chr2:54654200-54658200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr2:54654200-54660200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:54654400-54658400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:54654400-54660600	Enhancers	Fetal Brain Male	brain
10	chr2:54654600-54658400	Enhancers	Fetal Stomach	stomach
11	chr2:54654800-54656800	Weak transcription	Right Atrium	heart
12	chr2:54654800-54657600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:54654800-54660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:54655000-54656400	Weak transcription	Spleen	Spleen
15	chr2:54655000-54658200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:54655200-54657000	Enhancers	Fetal Kidney	kidney
17	chr2:54655200-54657600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:54655200-54659000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:54655200-54659800	Enhancers	Stomach Smooth Muscle	stomach
20	chr2:54655200-54660400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:54655400-54657000	Enhancers	Osteobl	bone
22	chr2:54655400-54658400	Enhancers	Placenta	Placenta
23	chr2:54655400-54658400	Enhancers	HUVEC	blood vessel
24	chr2:54655400-54658600	Enhancers	Ovary	ovary
25	chr2:54655600-54656800	Enhancers	NHDF-Ad	bronchial
26	chr2:54655600-54657000	Enhancers	Rectal Smooth Muscle	rectum
27	chr2:54655600-54657200	Enhancers	NHLF	lung
28	chr2:54655800-54656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:54655800-54656800	Flanking Active TSS	Fetal Lung	lung
30	chr2:54655800-54656800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:54655800-54657200	Enhancers	Colon Smooth Muscle	Colon
32	chr2:54656000-54657200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:54656000-54657200	Weak transcription	Psoas Muscle	Psoas
34	chr2:54656000-54660200	Enhancers	Fetal Heart	heart
35	chr2:54656200-54656600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54656200-54656600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:54656200-54657200	Weak transcription	HSMMtube	muscle
38	chr2:54656200-54660200	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links