Variant report

Variant	rs7133330
Chromosome Location	chr12:4461485-4461486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11063081	0.94[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11063105	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11063110	0.83[EUR][1000 genomes]
rs11063112	0.85[GIH][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12230757	0.86[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12231368	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819556	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819956	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823931	0.95[LWK][hapmap]
rs13312789	0.80[LWK][hapmap]
rs7296163	0.84[CEU][hapmap]
rs7955866	0.89[LWK][hapmap]
rs7961824	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv468985	chr12:4423612-4473329	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv557122	chr12:4423612-4473329	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv275025	chr12:4441705-4462505	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv519278	chr12:4441906-4475194	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7133330	C12orf5	Cis_1M	lymphoblastoid	RTeQTL
rs7133330	LRRC23	cis	parietal	SCAN
rs7133330	FGF6	cis	cerebellum	SCAN
rs7133330	CLEC4A	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4431200-4465800	Weak transcription	Psoas Muscle	Psoas
2	chr12:4431600-4462200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:4431600-4463400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:4431600-4465000	Weak transcription	Pancreas	Pancrea
5	chr12:4432200-4463400	Weak transcription	Small Intestine	intestine
6	chr12:4432200-4463600	Weak transcription	Colonic Mucosa	Colon
7	chr12:4433200-4463200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:4434000-4461600	Weak transcription	NHLF	lung
9	chr12:4434000-4465000	Weak transcription	Esophagus	oesophagus
10	chr12:4441000-4465600	Weak transcription	Fetal Intestine Large	intestine
11	chr12:4441800-4463600	Weak transcription	Brain Substantia Nigra	brain
12	chr12:4443400-4464800	Weak transcription	Fetal Brain Male	brain
13	chr12:4443600-4463400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:4447400-4464800	Weak transcription	Right Ventricle	heart
15	chr12:4447600-4462600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:4447600-4464400	Weak transcription	Spleen	Spleen
17	chr12:4447600-4464800	Weak transcription	Brain Germinal Matrix	brain
18	chr12:4447800-4464200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:4448000-4461800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:4448000-4462600	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:4448000-4464800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:4448600-4462600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:4449000-4463800	Weak transcription	Brain Anterior Caudate	brain
24	chr12:4449200-4462200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:4449200-4465000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:4449400-4466000	Weak transcription	NHDF-Ad	bronchial
27	chr12:4450000-4465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:4455600-4465000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:4456000-4462600	Strong transcription	Primary B cells from cord blood	blood
30	chr12:4456000-4462600	Strong transcription	HSMM	muscle
31	chr12:4456000-4463000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:4456000-4463600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:4456000-4463800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:4456000-4463800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:4456000-4463800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:4456000-4463800	Strong transcription	HMEC	breast
37	chr12:4456000-4464000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:4456000-4464800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:4456000-4464800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:4456000-4465200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:4456400-4464800	Weak transcription	Brain Angular Gyrus	brain
42	chr12:4457600-4462800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:4457600-4462800	Strong transcription	GM12878-XiMat	blood
44	chr12:4457600-4463600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:4457600-4463800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:4457600-4463800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:4457600-4464000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:4457800-4463800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:4458000-4462000	Strong transcription	Placenta	Placenta
50	chr12:4458000-4462600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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