Variant report

Variant	rs4964310
Chromosome Location	chr12:105394845-105394846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105379990..105383317-chr12:105392457..105395172,3	MCF-7	breast:
2	chr12:105394211..105395980-chr12:105415862..105418537,2	K562	blood:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10746008	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10778358	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs11112253	0.82[ASN][1000 genomes]
rs11112320	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112321	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112322	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610388	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12818323	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2249454	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs34337968	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4388976	0.87[JPT][hapmap]
rs4393404	0.87[JPT][hapmap]
rs4964120	0.83[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs4964316	0.83[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs6539171	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7135015	0.87[JPT][hapmap]
rs7313529	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73193606	0.82[ASN][1000 genomes]
rs7485673	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs7968763	0.84[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4964310	TCP11L2	cis	parietal	SCAN
rs4964310	C12orf45	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105381800-105398000	Strong transcription	A549	lung
2	chr12:105381800-105407400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:105381800-105411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:105382000-105397800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:105382000-105401400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:105382000-105401400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:105382200-105395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:105382200-105395200	Strong transcription	Primary B cells from cord blood	blood
9	chr12:105382200-105395600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr12:105382200-105401400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:105382200-105402000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:105382200-105402000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:105382200-105402000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:105382200-105402600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:105382400-105401200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:105382400-105401400	Strong transcription	Liver	Liver
17	chr12:105382600-105397800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:105382800-105398000	Strong transcription	Adipose Nuclei	Adipose
19	chr12:105383000-105402000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:105383200-105396400	Strong transcription	Fetal Intestine Large	intestine
21	chr12:105383200-105398000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:105383400-105399000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:105383600-105401600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:105383800-105397800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:105383800-105401200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:105384000-105395000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:105384000-105402000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:105384800-105400000	Strong transcription	Brain Anterior Caudate	brain
29	chr12:105385200-105395000	Strong transcription	GM12878-XiMat	blood
30	chr12:105385800-105395200	Strong transcription	Fetal Kidney	kidney
31	chr12:105385800-105401400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:105385800-105408400	Weak transcription	Fetal Heart	heart
33	chr12:105387200-105396400	Weak transcription	Fetal Brain Male	brain
34	chr12:105387200-105397000	Weak transcription	Psoas Muscle	Psoas
35	chr12:105387200-105397200	Weak transcription	Small Intestine	intestine
36	chr12:105387400-105403000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:105387600-105395200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:105387600-105412200	Weak transcription	HepG2	liver
39	chr12:105389000-105430600	Weak transcription	Hela-S3	cervix
40	chr12:105389400-105406800	Weak transcription	NH-A	brain
41	chr12:105389400-105411200	Weak transcription	Osteobl	bone
42	chr12:105390200-105404000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:105390400-105395800	Weak transcription	Ovary	ovary
44	chr12:105390400-105397000	Weak transcription	HUVEC	blood vessel
45	chr12:105390600-105397000	Weak transcription	HSMMtube	muscle
46	chr12:105391000-105407400	Weak transcription	NHDF-Ad	bronchial
47	chr12:105391800-105398000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:105392000-105395200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:105392200-105399400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:105392200-105400600	Strong transcription	HMEC	breast

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