Variant report

Variant	rs525359
Chromosome Location	chr2:234760474-234760475
allele	C/T
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: 0)

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

rs_ID	r²[population]
rs12692249	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13003628	0.93[ASN][1000 genomes]
rs169925	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs213542	0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2215172	0.94[ASN][1000 genomes]
rs2286433	1.00[CEU][hapmap]
rs2302156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs503913	1.00[CEU][hapmap]
rs528971	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs531643	0.95[EUR][1000 genomes]
rs554699	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs556691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609942	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs619929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs637082	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638071	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648818	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs650570	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650700	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654279	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]
rs689101	0.96[EUR][1000 genomes]
rs7570755	0.92[CEU][hapmap]
rs7596657	0.93[ASN][1000 genomes]
rs887062	1.00[CEU][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

No data

Chromatin state (count:87 , 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	chr2:234742600-234760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:234742600-234760600	Strong transcription	NHEK	skin
9	chr2:234742600-234760800	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr2:234742800-234760600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:234742800-234760600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:234742800-234760800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:234743000-234760800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr2:234743000-234760800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:234743000-234761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:234743200-234760600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:234743200-234760600	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:234744000-234762400	Weak transcription	Small Intestine	intestine
19	chr2:234744600-234762000	Weak transcription	Colonic Mucosa	Colon
20	chr2:234748200-234760600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:234748400-234760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:234748600-234762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:234749200-234761600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:234749400-234760600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:234750600-234761400	Weak transcription	Fetal Brain Female	brain
26	chr2:234751200-234760800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:234752800-234761600	Weak transcription	Fetal Kidney	kidney
28	chr2:234753200-234760600	Weak transcription	Spleen	Spleen
29	chr2:234753200-234761600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:234753200-234762200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:234753600-234760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:234755000-234760600	Weak transcription	NH-A	brain
33	chr2:234755200-234761000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:234755200-234761000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:234755200-234761000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:234756600-234762600	Transcr. at gene 5' and 3'	A549	lung
37	chr2:234756800-234762000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:234757200-234761000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:234758200-234760600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:234758400-234760600	Genic enhancers	Fetal Thymus	thymus
41	chr2:234758400-234761600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:234758600-234760800	Weak transcription	Fetal Lung	lung
43	chr2:234758600-234761200	Enhancers	Fetal Heart	heart
44	chr2:234758600-234761200	Weak transcription	Fetal Intestine Large	intestine
45	chr2:234758600-234762000	Weak transcription	Placenta	Placenta
46	chr2:234758800-234760600	Weak transcription	Brain Germinal Matrix	brain
47	chr2:234759000-234760600	Weak transcription	NHLF	lung
48	chr2:234759000-234762600	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr2:234759200-234760600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:234759400-234760600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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