Variant report

Variant	rs12643013
Chromosome Location	chr4:144206948-144206949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10012713	0.93[ASN][1000 genomes]
rs10028909	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12501994	0.82[CHD][hapmap]
rs13118846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129434	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13136521	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs13137362	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1532981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686361	0.81[ASN][1000 genomes]
rs28589653	0.81[ASN][1000 genomes]
rs300890	0.83[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs300891	0.86[AMR][1000 genomes]
rs300892	0.86[AMR][1000 genomes]
rs300893	0.81[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs300895	0.81[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs300904	0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs300905	0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs300943	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs300946	0.95[ASN][1000 genomes]
rs300947	0.95[ASN][1000 genomes]
rs300951	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs300953	0.88[ASN][1000 genomes]
rs3846235	0.80[ASN][1000 genomes]
rs568685	0.83[AMR][1000 genomes]
rs592349	0.93[ASN][1000 genomes]
rs62337488	0.86[AMR][1000 genomes]
rs624189	0.87[AMR][1000 genomes]
rs6537152	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537153	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs666542	0.93[ASN][1000 genomes]
rs6823434	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6840603	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7655782	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690761	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv880177	chr4:144174773-144214082	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12643013	INPP4B	cis	cerebellum	SCAN
rs12643013	ZNF330	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144203200-144207200	Weak transcription	Psoas Muscle	Psoas
2	chr4:144203600-144207600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:144203800-144207200	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:144203800-144207400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:144204000-144207000	Weak transcription	Adipose Nuclei	Adipose
6	chr4:144204800-144208200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:144206000-144210200	Enhancers	Fetal Stomach	stomach
8	chr4:144206200-144207200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:144206200-144207200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:144206200-144209000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr4:144206400-144207000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:144206400-144207000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:144206400-144207000	Weak transcription	NHEK	skin
14	chr4:144206600-144207800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:144206600-144208800	Enhancers	Fetal Lung	lung
16	chr4:144206800-144207000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:144206800-144207200	Weak transcription	HMEC	breast
18	chr4:144206800-144207400	Enhancers	Osteobl	bone
19	chr4:144206800-144207800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:144206800-144207800	Enhancers	NHDF-Ad	bronchial
21	chr4:144206800-144208000	Enhancers	NHLF	lung
22	chr4:144206800-144208200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:144206800-144209000	Enhancers	Fetal Brain Male	brain
24	chr4:144206800-144209000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr4:144206800-144209200	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links