Variant report

Variant	rs2518683
Chromosome Location	chr22:29695929-29695930
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29666189..29669898-chr22:29695758..29699606,3	K562	blood:
2	chr22:29690273..29693453-chr22:29694062..29696820,3	MCF-7	breast:
3	chr22:29661802..29668258-chr22:29692795..29700190,12	K562	blood:
4	chr22:29684504..29686198-chr22:29694091..29696535,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182944	Chromatin interaction
ENSG00000100263	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11702906	0.84[YRI][hapmap]
rs11704551	1.00[CHD][hapmap]
rs131184	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs131190	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs140064	0.83[ASN][1000 genomes]
rs140065	0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs174760	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs174772	1.00[CHD][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap]
rs1894414	0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap]
rs2231398	0.82[CHB][hapmap];0.92[YRI][hapmap]
rs2857460	0.83[ASN][1000 genomes]
rs4823033	0.84[YRI][hapmap]
rs5997460	0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs8140836	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv2169204	chr22:29695811-29696217	Strong transcription Weak transcription	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a
7	esv3528711	chr22:29695883-29696135	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv3528713	chr22:29695916-29696094	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2518683	TUG1	cis	cerebellum	SCAN
rs2518683	NEFH	cis	parietal	SCAN
rs2518683	ADORA2A	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29667600-29697800	Strong transcription	Fetal Muscle Trunk	muscle
2	chr22:29667800-29697000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:29667800-29697200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29667800-29697800	Strong transcription	Fetal Thymus	thymus
5	chr22:29668000-29697000	Strong transcription	NHEK	skin
6	chr22:29668000-29697200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr22:29668000-29697200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr22:29668000-29697600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr22:29668000-29697600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr22:29668000-29698000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:29668000-29698200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr22:29668200-29697000	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr22:29668200-29697400	Strong transcription	HMEC	breast
14	chr22:29668200-29697600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr22:29668200-29697800	Strong transcription	Fetal Muscle Leg	muscle
16	chr22:29668200-29698000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr22:29668200-29698400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:29668200-29698400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr22:29668400-29697200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr22:29668400-29698000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr22:29668600-29697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr22:29668600-29698000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr22:29668800-29697000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr22:29668800-29697000	Strong transcription	Fetal Lung	lung
25	chr22:29668800-29697200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr22:29668800-29697200	Strong transcription	Osteobl	bone
27	chr22:29668800-29697800	Strong transcription	HSMM	muscle
28	chr22:29669000-29696000	Strong transcription	HUVEC	blood vessel
29	chr22:29669000-29697200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:29669000-29697200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:29669000-29697200	Strong transcription	NH-A	brain
32	chr22:29669000-29698400	Strong transcription	Thymus	Thymus
33	chr22:29669200-29697200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr22:29669200-29698000	Strong transcription	Fetal Brain Female	brain
35	chr22:29669400-29696600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr22:29669400-29697000	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr22:29669400-29697400	Strong transcription	NHLF	lung
38	chr22:29669400-29698400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr22:29669400-29698400	Strong transcription	Brain Germinal Matrix	brain
40	chr22:29669600-29697000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr22:29669600-29697200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr22:29670400-29697600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr22:29670600-29702400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr22:29671800-29697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr22:29672200-29697400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr22:29672600-29698800	Strong transcription	Fetal Stomach	stomach
47	chr22:29672800-29697600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:29673200-29697000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr22:29673200-29697000	Strong transcription	Left Ventricle	heart
50	chr22:29673200-29697000	Strong transcription	HepG2	liver

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