Variant report

Variant	rs3751275
Chromosome Location	chr12:51518787-51518788
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51475824..51478649-chr12:51516706..51519135,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10876140	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1112391	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs11169689	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11169691	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11169692	0.87[EUR][1000 genomes]
rs12582592	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs17125286	0.81[CEU][hapmap]
rs17125346	0.81[CEU][hapmap]
rs17125375	0.81[CEU][hapmap]
rs17125401	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs2018022	0.84[TSI][hapmap]
rs2306732	0.85[JPT][hapmap]
rs3190077	1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs3759406	0.81[CEU][hapmap]
rs55938119	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66781280	0.89[EUR][1000 genomes]
rs7722	0.85[JPT][hapmap]

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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv983323	chr12:51518356-51519057	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3751275	CCNT1	cis	parietal	SCAN
rs3751275	TFCP2	cis	multi-tissue	Pritchard
rs3751275	TFCP2	trans	brain	seeQTL
rs3751275	TFCP2	cis	brain	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:51488400-51526600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:51496400-51523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:51501000-51521000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:51502200-51527200	Weak transcription	Colonic Mucosa	Colon
7	chr12:51502800-51531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
9	chr12:51503600-51532000	Weak transcription	Brain Angular Gyrus	brain
10	chr12:51504800-51518800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:51507600-51519800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:51507800-51532200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:51507800-51539800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:51508000-51543000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:51509600-51520800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:51510200-51519200	Weak transcription	Fetal Heart	heart
18	chr12:51510200-51520400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:51510200-51526000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:51510200-51536200	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:51510200-51554400	Weak transcription	K562	blood
22	chr12:51511400-51520800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:51511400-51531400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:51511400-51558800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:51512600-51519200	Weak transcription	Small Intestine	intestine
26	chr12:51512800-51519800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:51512800-51535600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:51513000-51520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:51513000-51532200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr12:51513000-51565400	Weak transcription	Fetal Lung	lung
31	chr12:51513200-51518800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:51513200-51518800	Weak transcription	HSMM	muscle
33	chr12:51513200-51520000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:51513200-51520200	Weak transcription	Osteobl	bone
35	chr12:51513200-51522600	Weak transcription	NH-A	brain
36	chr12:51513200-51524200	Weak transcription	Fetal Brain Male	brain
37	chr12:51513200-51531600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:51513400-51520000	Weak transcription	HMEC	breast
39	chr12:51513400-51527800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:51514400-51532200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:51517000-51519200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:51517200-51518800	Weak transcription	Hela-S3	cervix
43	chr12:51517200-51521000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:51517200-51547600	Weak transcription	Fetal Kidney	kidney
45	chr12:51517200-51554600	Weak transcription	HepG2	liver
46	chr12:51517400-51519200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:51517400-51519400	Strong transcription	Primary T cells from cord blood	blood
48	chr12:51517600-51519200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:51517600-51519200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:51517600-51519200	Strong transcription	A549	lung

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