Variant report

Variant	rs2540993
Chromosome Location	chr2:37298750-37298751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37297161..37300083-chr2:37309727..37312346,2	K562	blood:
2	chr2:37291968..37296809-chr2:37296827..37300511,4	K562	blood:
3	chr2:37298361..37300896-chr2:37301452..37303760,2	MCF-7	breast:
4	chr2:37296556..37299505-chr2:37305358..37308642,3	K562	blood:

Variant related genes	Relation type
ENSG00000008869	Chromatin interaction
ENSG00000152133	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153588	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11124559	1.00[EUR][1000 genomes]
rs2307477	1.00[EUR][1000 genomes]
rs2540994	1.00[EUR][1000 genomes]
rs2706806	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2706807	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2888443	1.00[EUR][1000 genomes]
rs3845782	0.81[YRI][hapmap]
rs4503966	1.00[EUR][1000 genomes]
rs4670653	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4670654	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6709976	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6734153	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs6734269	0.87[AFR][1000 genomes]
rs6743906	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73924975	1.00[EUR][1000 genomes]
rs73927404	1.00[EUR][1000 genomes]
rs7596489	0.91[YRI][hapmap];0.83[AFR][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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv873879	chr2:37200033-37299145	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37221000-37307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:37223400-37300400	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr2:37240400-37304800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:37240600-37306000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:37240800-37306400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:37240800-37307000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:37241200-37306000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:37241400-37299600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:37242200-37305800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:37253800-37310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:37272400-37306400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:37272600-37299400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:37272600-37309800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:37274200-37308800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:37274400-37299200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:37274400-37309600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:37275200-37300200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:37275200-37307000	Strong transcription	Adipose Nuclei	Adipose
19	chr2:37275400-37299400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:37275400-37309200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:37276800-37299400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:37277600-37299400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:37278000-37299600	Strong transcription	Liver	Liver
24	chr2:37278600-37310800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:37279200-37300200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:37279200-37309200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:37279400-37307600	Strong transcription	Fetal Intestine Large	intestine
28	chr2:37281800-37307200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:37282000-37308400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:37284600-37307200	Weak transcription	Stomach Mucosa	stomach
31	chr2:37285600-37299800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:37285800-37299400	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:37287000-37299400	Strong transcription	Brain Hippocampus Middle	brain
34	chr2:37287000-37305200	Strong transcription	Primary T cells from cord blood	blood
35	chr2:37287400-37309200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:37287600-37306000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:37287600-37309600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:37287800-37306600	Strong transcription	Primary B cells from cord blood	blood
39	chr2:37288600-37299400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:37289000-37299200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:37289000-37299800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:37289000-37309400	Strong transcription	Fetal Thymus	thymus
43	chr2:37289200-37299200	Strong transcription	Fetal Intestine Small	intestine
44	chr2:37289400-37299400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:37289400-37307600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr2:37289600-37299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:37289600-37299800	Strong transcription	Dnd41	blood
48	chr2:37289600-37299800	Strong transcription	HepG2	liver
49	chr2:37289800-37306400	Strong transcription	Brain Anterior Caudate	brain
50	chr2:37290000-37307400	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links