Variant report

Variant	rs654279
Chromosome Location	chr2:234760782-234760783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234758197..234760837-chr2:234836027..234838488,2	K562	blood:
2	chr2:234399142..234401068-chr2:234759873..234762356,2	MCF-7	breast:
3	chr2:234759783..234762312-chr2:234875051..234877633,2	K562	blood:
4	chr2:234753471..234756128-chr2:234758714..234761959,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144481	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12692249	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13003628	0.93[ASN][1000 genomes]
rs169925	0.96[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs213542	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2215172	0.94[ASN][1000 genomes]
rs2286433	1.00[CEU][hapmap]
rs2302156	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs503913	1.00[CEU][hapmap]
rs525359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528971	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs531643	0.95[EUR][1000 genomes]
rs554699	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs556691	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609942	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs619929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs626110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs637082	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638071	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648818	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs650570	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650700	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689101	0.96[EUR][1000 genomes]
rs7570755	0.91[CEU][hapmap]
rs7596657	0.93[ASN][1000 genomes]
rs887062	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs654279	NCL	cis	parietal	SCAN
rs654279	SNORD20	cis	cerebellum	SCAN
rs654279	CAB39	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
2	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
3	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
4	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
5	chr2:234741800-234762000	Weak transcription	Gastric	stomach
6	chr2:234742200-234762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
13	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
14	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:234749200-234761600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:234750600-234761400	Weak transcription	Fetal Brain Female	brain
17	chr2:234751200-234760800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:234752800-234761600	Weak transcription	Fetal Kidney	kidney
19	chr2:234753200-234761600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:234753200-234762200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:234755200-234761000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:234755200-234761000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:234755200-234761000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:234756600-234762600	Transcr. at gene 5' and 3'	A549	lung
25	chr2:234756800-234762000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:234757200-234761000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:234758400-234761600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:234758600-234760800	Weak transcription	Fetal Lung	lung
29	chr2:234758600-234761200	Enhancers	Fetal Heart	heart
30	chr2:234758600-234761200	Weak transcription	Fetal Intestine Large	intestine
31	chr2:234758600-234762000	Weak transcription	Placenta	Placenta
32	chr2:234759000-234762600	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr2:234759400-234760800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:234759400-234761800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr2:234759600-234761800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:234760400-234760800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:234760400-234760800	Genic enhancers	K562	blood
38	chr2:234760400-234761000	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:234760400-234761000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:234760400-234761000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:234760400-234761000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr2:234760400-234761000	Genic enhancers	HMEC	breast
43	chr2:234760400-234761200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:234760400-234761200	Genic enhancers	Fetal Stomach	stomach
45	chr2:234760400-234762200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr2:234760400-234762400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:234760400-234762400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
48	chr2:234760400-234763000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:234760600-234760800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:234760600-234760800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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