Variant report

Variant	rs17039541
Chromosome Location	chr2:54333572-54333573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54333529..54340855-chr2:54341009..54344742,14	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10177109	1.00[AMR][1000 genomes]
rs10496027	0.91[ASW][hapmap];0.90[YRI][hapmap]
rs11884857	0.95[YRI][hapmap]
rs11889527	0.95[YRI][hapmap]
rs11904365	0.95[YRI][hapmap]
rs57045403	1.00[AMR][1000 genomes]
rs6706299	1.00[AMR][1000 genomes]
rs6707794	0.85[AMR][1000 genomes]
rs6711310	0.85[AMR][1000 genomes]
rs6722291	1.00[AMR][1000 genomes]
rs72906742	1.00[AMR][1000 genomes]
rs72906760	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72906777	1.00[AMR][1000 genomes]
rs72908707	0.87[AMR][1000 genomes]
rs72908720	1.00[AMR][1000 genomes]
rs7559651	0.90[YRI][hapmap]
rs7559709	1.00[AMR][1000 genomes]
rs7574917	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:54324000-54334400	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:54325800-54334400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:54326000-54334000	Weak transcription	Brain Substantia Nigra	brain
5	chr2:54331200-54335000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54331200-54342000	Weak transcription	Psoas Muscle	Psoas
7	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
8	chr2:54331400-54333600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:54331400-54333600	Weak transcription	K562	blood
10	chr2:54331400-54334000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:54331400-54334000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:54331400-54334000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:54331400-54334000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:54331400-54334000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:54331400-54334000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:54331400-54334000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:54331400-54334000	Weak transcription	Thymus	Thymus
18	chr2:54331400-54334000	Weak transcription	HSMMtube	muscle
19	chr2:54331400-54334400	Weak transcription	Adipose Nuclei	Adipose
20	chr2:54331400-54334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:54331400-54334600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:54331400-54334800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:54331400-54334800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:54331400-54335000	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:54331400-54335200	Weak transcription	Fetal Heart	heart
26	chr2:54331400-54335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:54331400-54335800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:54331400-54335800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
30	chr2:54331600-54334000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:54331600-54334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:54331600-54334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:54331600-54334200	Weak transcription	HUVEC	blood vessel
34	chr2:54331600-54334600	Weak transcription	NHDF-Ad	bronchial
35	chr2:54331600-54335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:54331800-54334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:54331800-54334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:54331800-54335000	Weak transcription	NHEK	skin
39	chr2:54332000-54333600	Weak transcription	A549	lung
40	chr2:54332000-54333800	Weak transcription	HepG2	liver
41	chr2:54332000-54334000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:54332000-54334200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:54332000-54335200	Weak transcription	HMEC	breast
44	chr2:54332200-54334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:54332400-54333600	Weak transcription	Liver	Liver
46	chr2:54332400-54334000	Weak transcription	Hela-S3	cervix
47	chr2:54332400-54334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:54332400-54335000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:54333400-54333800	Weak transcription	Primary B cells from cord blood	blood

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