Variant report

Variant	rs213545
Chromosome Location	chr2:234775941-234775942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
2	chr2:234773117..234776003-chr2:234811783..234814431,2	K562	blood:
3	chr2:234766693..234769626-chr2:234773837..234776124,2	MCF-7	breast:
4	2:234635414-234639782..2:234772667-234780240	Hela-S3	cervix:
5	chr2:234600369..234602177-chr2:234775436..234777156,2	MCF-7	breast:
6	2:234683624-234705119..2:234772667-234780240	Hela-S3	cervix:
7	2:234772667-234780240..2:234954947-234965240	Hela-S3	cervix:
8	2:234543708-234558325..2:234772667-234780240	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000234143	Chromatin interaction
ENSG00000185038	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000072080	Chromatin interaction
ENSG00000243135	Chromatin interaction
ENSG00000242515	Chromatin interaction
ENSG00000128534	Chromatin interaction
ENSG00000241635	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12692249	0.97[ASN][1000 genomes]
rs13003628	0.91[EUR][1000 genomes]
rs169922	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169925	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs183331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213542	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2215172	0.91[EUR][1000 genomes]
rs4663339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs503913	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs528971	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs531643	0.97[ASN][1000 genomes]
rs554699	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs609942	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6431643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431644	0.88[CEU][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648818	0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs689101	0.97[ASN][1000 genomes]
rs7596657	0.91[EUR][1000 genomes]
rs887062	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs213545	MSL3P1	cis	Thyroid	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234763600-234776800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:234763800-234776600	Weak transcription	Right Ventricle	heart
3	chr2:234764000-234776400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:234764000-234776600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:234764000-234776600	Weak transcription	HUVEC	blood vessel
6	chr2:234764200-234776600	Weak transcription	Primary B cells from cord blood	blood
7	chr2:234764200-234776600	Weak transcription	Primary T cells from cord blood	blood
8	chr2:234764200-234776600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:234764200-234776600	Weak transcription	HMEC	breast
10	chr2:234764200-234776600	Weak transcription	NH-A	brain
11	chr2:234764200-234776600	Weak transcription	NHDF-Ad	bronchial
12	chr2:234764200-234776600	Weak transcription	NHEK	skin
13	chr2:234764200-234776800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:234764400-234776400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:234764400-234776600	Weak transcription	HSMM	muscle
16	chr2:234767000-234776600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:234771200-234776800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:234773000-234776000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:234773800-234776600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:234774200-234776600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:234774400-234776000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:234774400-234776000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:234774400-234776000	ZNF genes & repeats	A549	lung
24	chr2:234774400-234776200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:234774600-234776000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:234774600-234776800	ZNF genes & repeats	Placenta	Placenta
27	chr2:234774800-234776000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:234774800-234776000	Strong transcription	Osteobl	bone
29	chr2:234775000-234776000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:234775000-234776400	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr2:234775000-234776600	Weak transcription	Fetal Lung	lung
32	chr2:234775000-234776800	ZNF genes & repeats	Fetal Stomach	stomach
33	chr2:234775200-234776000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:234775200-234776200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:234775200-234776600	Weak transcription	HSMMtube	muscle
36	chr2:234775200-234777400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:234775400-234776000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr2:234775400-234776600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:234775400-234776600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:234775400-234776600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:234775400-234776600	Weak transcription	Fetal Brain Male	brain
42	chr2:234775400-234776600	Weak transcription	Gastric	stomach
43	chr2:234775400-234776600	Weak transcription	Lung	lung
44	chr2:234775600-234776200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:234775600-234776600	Weak transcription	NHLF	lung
46	chr2:234775600-234777200	Active TSS	Hela-S3	cervix
47	chr2:234775800-234776000	Weak transcription	K562	blood
48	chr2:234775800-234776400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:234775800-234776400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:234775800-234776400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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