Variant report

Variant	rs2133943
Chromosome Location	chr12:32654210-32654211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:32654055-32656593	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32652717..32654744-chr12:32667821..32669805,2	K562	blood:

Variant related genes	Relation type
FGD4	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10506090	0.82[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10506093	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771960	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771961	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10771962	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844222	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10844223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844224	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10844226	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844227	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844228	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10844229	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10844230	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844231	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844234	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11052046	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11052052	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11052053	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11052055	0.81[MEX][hapmap]
rs11608343	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1500875	0.82[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1500876	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17536908	0.81[MEX][hapmap]
rs4520681	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61928965	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7308163	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7962342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964715	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7967306	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7967702	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7974089	0.96[AMR][1000 genomes];0.87[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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2133943	FGD4	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
2	chr12:32625000-32655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:32625200-32655200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:32634000-32655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:32639000-32655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:32644800-32654400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:32648200-32654400	Weak transcription	HMEC	breast
8	chr12:32648200-32655600	Weak transcription	NHEK	skin
9	chr12:32648200-32657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
11	chr12:32649600-32658200	Weak transcription	Primary T cells from cord blood	blood
12	chr12:32650600-32656200	Enhancers	Fetal Heart	heart
13	chr12:32650800-32659200	Weak transcription	Aorta	Aorta
14	chr12:32651000-32654600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:32651000-32654800	Enhancers	Fetal Intestine Small	intestine
16	chr12:32651200-32654600	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:32651200-32654800	Weak transcription	Fetal Thymus	thymus
18	chr12:32651200-32658000	Weak transcription	Primary B cells from cord blood	blood
19	chr12:32651400-32654600	Weak transcription	Brain Anterior Caudate	brain
20	chr12:32651400-32654800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:32651400-32655000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:32651400-32658000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:32651800-32654800	Enhancers	Fetal Intestine Large	intestine
24	chr12:32652200-32654400	Weak transcription	Fetal Lung	lung
25	chr12:32652400-32654600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:32652400-32654800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:32652400-32654800	Weak transcription	HUVEC	blood vessel
28	chr12:32652600-32654800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:32652600-32654800	Enhancers	Left Ventricle	heart
30	chr12:32652800-32654800	Weak transcription	Psoas Muscle	Psoas
31	chr12:32653200-32654800	Weak transcription	Right Ventricle	heart
32	chr12:32653600-32655000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:32653600-32655000	Enhancers	HepG2	liver
34	chr12:32653600-32656600	Enhancers	Pancreas	Pancrea
35	chr12:32653800-32654600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:32653800-32654600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr12:32653800-32654600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:32653800-32654600	Enhancers	Fetal Muscle Leg	muscle
39	chr12:32653800-32654800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:32653800-32654800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:32653800-32654800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr12:32653800-32654800	Enhancers	Adipose Nuclei	Adipose
43	chr12:32653800-32654800	Enhancers	Liver	Liver
44	chr12:32653800-32654800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:32653800-32654800	Enhancers	Brain Substantia Nigra	brain
46	chr12:32653800-32654800	Enhancers	Ovary	ovary
47	chr12:32653800-32654800	Enhancers	Right Atrium	heart
48	chr12:32653800-32654800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:32653800-32655000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr12:32653800-32655000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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