Variant report

Variant	rs2289879
Chromosome Location	chr5:50265086-50265087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr5:50264730-50265502	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr5:50265078-50265273	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
4	GATA3	chr5:50264851-50265121	SH-SY5Y	brain:	n/a	chr5:50264859-50264868
5	GATA2	chr5:50263552-50266094	SH-SY5Y	brain:	n/a	chr5:50264176-50264197 chr5:50264179-50264195 chr5:50264183-50264192 chr5:50264183-50264192 chr5:50264164-50264171 chr5:50263968-50263975 chr5:50264179-50264195 chr5:50264859-50264868 chr5:50264182-50264192 chr5:50266034-50266043
6	MAX	chr5:50265036-50265603	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:50264751-50265788	H1-neurons	neurons:	n/a	n/a
8	MAX	chr5:50265049-50265587	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr5:50265035-50265522	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTBP2	chr5:50265045-50266075	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr5:50265029-50265544	SK-N-SH	brain:	n/a	chr5:50265442-50265452
12	E2F6	chr5:50264955-50265741	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr5:50261713-50266474	H1-neurons	neurons:	n/a	chr5:50264435-50264449 chr5:50264118-50264138 chr5:50264118-50264138 chr5:50265442-50265452 chr5:50264121-50264134
14	POLR2A	chr5:50264923-50266294	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMB-3	chr5:50265051-50265157	ENSG00000251573
2	lnc-EMB-3	chr5:50265051-50265411	ENSG00000251573
3	lnc-EMB-3	chr5:50265051-50265411	NR_104653

Variant related genes	Relation type
ENSG00000248918	TF binding region
ENSG00000250360	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10434565	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10805506	0.94[ASN][1000 genomes]
rs10940613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523135	0.82[ASN][1000 genomes]
rs12657116	0.96[ASN][1000 genomes]
rs12658921	0.86[ASN][1000 genomes]
rs12659587	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs13162201	0.86[ASN][1000 genomes]
rs13175573	0.88[ASN][1000 genomes]
rs13177246	1.00[ASN][1000 genomes]
rs1423227	0.98[ASN][1000 genomes]
rs1545350	0.88[ASN][1000 genomes]
rs16888260	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2289880	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs250216	1.00[ASN][1000 genomes]
rs250238	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs35192063	1.00[ASN][1000 genomes]
rs35477295	1.00[ASN][1000 genomes]
rs35894462	1.00[ASN][1000 genomes]
rs3843453	0.85[JPT][hapmap]
rs4866019	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs4866020	1.00[ASN][1000 genomes]
rs59135537	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs622304	0.83[ASN][1000 genomes]
rs66947818	0.87[ASN][1000 genomes]
rs679362	0.83[ASN][1000 genomes]
rs71615992	0.84[ASN][1000 genomes]
rs71615994	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:50261400-50266400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:50261400-50266400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr5:50262600-50265200	Bivalent/Poised TSS	NHDF-Ad	bronchial
5	chr5:50262600-50266000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr5:50262600-50266200	Bivalent/Poised TSS	Fetal Stomach	stomach
7	chr5:50262800-50265200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:50262800-50265200	Bivalent/Poised TSS	Psoas Muscle	Psoas
9	chr5:50262800-50265400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr5:50262800-50266200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
11	chr5:50263000-50265200	Active TSS	Right Atrium	heart
12	chr5:50263000-50266000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr5:50263000-50266000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
14	chr5:50263200-50265600	Active TSS	Stomach Smooth Muscle	stomach
15	chr5:50263200-50265800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
16	chr5:50263200-50265800	Bivalent Enhancer	Fetal Heart	heart
17	chr5:50263200-50266000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr5:50263200-50266000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr5:50263400-50265400	Flanking Bivalent TSS/Enh	Liver	Liver
20	chr5:50263400-50265600	Bivalent/Poised TSS	Aorta	Aorta
21	chr5:50263400-50265800	Bivalent Enhancer	Fetal Brain Male	brain
22	chr5:50263400-50265800	Active TSS	Gastric	stomach
23	chr5:50263400-50266000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:50263600-50265200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:50263600-50266000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr5:50263600-50266000	Bivalent Enhancer	Fetal Lung	lung
27	chr5:50263800-50265200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
28	chr5:50263800-50265200	Bivalent Enhancer	Fetal Intestine Small	intestine
29	chr5:50263800-50265200	Enhancers	Pancreas	Pancrea
30	chr5:50263800-50265400	Bivalent Enhancer	Fetal Intestine Large	intestine
31	chr5:50263800-50265600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:50263800-50265600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
33	chr5:50263800-50265600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
34	chr5:50263800-50265800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr5:50263800-50265800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr5:50263800-50266000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr5:50263800-50266000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr5:50263800-50266000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
39	chr5:50263800-50266200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr5:50263800-50266400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
41	chr5:50264000-50265200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:50264000-50265200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:50264000-50265200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr5:50264000-50265400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:50264000-50265400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
46	chr5:50264000-50266000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:50264000-50266000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:50264200-50265200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr5:50264200-50265600	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
50	chr5:50264200-50266000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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