Variant report

Variant	rs2124949
Chromosome Location	chr5:52884752-52884753
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13190354	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1388111	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2087619	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4147737	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147738	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147743	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs501403	0.87[ASN][1000 genomes]
rs56099109	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56291043	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62370277	0.80[AMR][1000 genomes]
rs62370279	0.80[AMR][1000 genomes]
rs72750150	0.94[ASN][1000 genomes]
rs72751831	0.94[ASN][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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52857800-52892800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:52857800-52898800	Weak transcription	HSMM	muscle
3	chr5:52858000-52899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:52858000-52900400	Weak transcription	Fetal Kidney	kidney
5	chr5:52858200-52885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:52858200-52897200	Weak transcription	NHEK	skin
7	chr5:52858400-52895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:52858400-52899800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:52860000-52909000	Weak transcription	Small Intestine	intestine
10	chr5:52860200-52885600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:52860600-52884800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:52861600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:52865000-52900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:52865200-52885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:52865600-52898400	Weak transcription	Fetal Lung	lung
16	chr5:52865600-52899800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:52867600-52888400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:52868200-52885200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:52869600-52896000	Weak transcription	Fetal Stomach	stomach
20	chr5:52870200-52892000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:52872000-52892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:52872200-52885000	Weak transcription	Primary T cells from cord blood	blood
23	chr5:52873000-52884800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:52873000-52887000	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:52873000-52889200	Weak transcription	A549	lung
26	chr5:52873000-52900400	Weak transcription	Gastric	stomach
27	chr5:52873200-52899000	Weak transcription	Right Atrium	heart
28	chr5:52873400-52885400	Weak transcription	Left Ventricle	heart
29	chr5:52873400-52889800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:52874400-52885200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:52874400-52888400	Weak transcription	Fetal Heart	heart
32	chr5:52874600-52889800	Weak transcription	HepG2	liver
33	chr5:52875000-52885400	Weak transcription	Aorta	Aorta
34	chr5:52875000-52900000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:52875400-52899200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:52875600-52889400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:52876800-52907400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:52877200-52884800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:52877400-52885800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:52877400-52900400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:52877600-52898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:52878400-52885400	Weak transcription	Psoas Muscle	Psoas
43	chr5:52878400-52899000	Weak transcription	Ovary	ovary
44	chr5:52878400-52901200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:52879600-52895200	Weak transcription	Fetal Intestine Large	intestine
46	chr5:52883000-52900200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:52883400-52893000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:52884200-52885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:52884200-52900400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr5:52884400-52885000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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