Variant report

Variant	rs2289880
Chromosome Location	chr5:50265880-50265881
allele	G/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	BACH1	chr5:50265602-50266106	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr5:50262485-50266469	NT2-D1	testis:	n/a	n/a
3	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
4	CTBP2	chr5:50265045-50266075	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr5:50261713-50266474	H1-neurons	neurons:	n/a	chr5:50264435-50264449 chr5:50264118-50264138 chr5:50264118-50264138 chr5:50265442-50265452 chr5:50264121-50264134
6	POLR2A	chr5:50264923-50266294	H1-neurons	neurons:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EMB-3	chr5:50265757-50266001	ENSG00000251573
2	lnc-PARP8-2	chr5:50265757-50272447	NONHSAT101376
3	lnc-EMB-3	chr5:50265757-50266021	NR_104653

Variant related genes	Relation type
ENSG00000250360	TF binding region
ENSG00000251573	TF binding region

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10805506	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10940613	1.00[ASN][1000 genomes]
rs12523135	0.82[ASN][1000 genomes]
rs12657116	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12658921	0.86[ASN][1000 genomes]
rs12659587	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162201	0.86[ASN][1000 genomes]
rs13175573	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13177246	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182809	0.98[EUR][1000 genomes]
rs1423227	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545350	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2289879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs250216	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250238	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs35192063	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35477295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894462	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843453	0.85[JPT][hapmap]
rs4866019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59135537	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:62 , 50 per page) page: 1 2

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	chr5:50262600-50266000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
5	chr5:50262600-50266200	Bivalent/Poised TSS	Fetal Stomach	stomach
6	chr5:50262800-50266200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
7	chr5:50263000-50266000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
8	chr5:50263000-50266000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr5:50263200-50266000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr5:50263200-50266000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
11	chr5:50263400-50266000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:50263600-50266000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr5:50263600-50266000	Bivalent Enhancer	Fetal Lung	lung
14	chr5:50263800-50266000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr5:50263800-50266000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
16	chr5:50263800-50266000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
17	chr5:50263800-50266200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr5:50263800-50266400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
19	chr5:50264000-50266000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:50264000-50266000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:50264200-50266000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:50264200-50266000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:50264200-50266000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr5:50264400-50266000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:50264400-50266000	Bivalent Enhancer	Primary T cells from cord blood	blood
26	chr5:50264400-50266000	Bivalent Enhancer	Spleen	Spleen
27	chr5:50264600-50266200	Bivalent/Poised TSS	Fetal Thymus	thymus
28	chr5:50264800-50266000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:50264800-50266000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:50264800-50266200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr5:50264800-50266400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr5:50264800-50266600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:50265000-50266000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
34	chr5:50265000-50266200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:50265000-50266400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:50265200-50266000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
37	chr5:50265200-50266200	Bivalent/Poised TSS	Thymus	Thymus
38	chr5:50265400-50266000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:50265400-50266000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:50265400-50266000	Bivalent Enhancer	Liver	Liver
41	chr5:50265400-50266000	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr5:50265400-50266200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr5:50265400-50266200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:50265400-50266200	Bivalent Enhancer	Fetal Brain Female	brain
45	chr5:50265600-50266000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:50265600-50266000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
47	chr5:50265600-50266200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
48	chr5:50265800-50266000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:50265800-50266000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:50265800-50266000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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