Variant report

Variant	rs319939
Chromosome Location	chr12:51346573-51346574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10783408	0.91[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs10783409	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10783410	0.87[CEU][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876121	0.85[ASN][1000 genomes]
rs10876123	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876128	0.85[CEU][hapmap]
rs10876130	0.81[CEU][hapmap]
rs10876131	0.84[CEU][hapmap]
rs10876136	0.81[CEU][hapmap]
rs12424509	0.84[CEU][hapmap]
rs12809226	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12823317	0.96[ASN][1000 genomes]
rs149411	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs15756	0.85[CEU][hapmap]
rs1632791	0.83[CEU][hapmap]
rs2029145	0.87[CEU][hapmap]
rs2029146	0.85[CEU][hapmap]
rs224572	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap]
rs224575	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2359187	0.94[ASN][1000 genomes]
rs2544019	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554856	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2630371	0.82[EUR][1000 genomes]
rs319931	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs370462	0.85[CEU][hapmap]
rs427020	0.87[CEU][hapmap]
rs4438107	0.81[CEU][hapmap]
rs6580782	0.84[CEU][hapmap]
rs6580785	0.81[CEU][hapmap]
rs6580788	0.81[CEU][hapmap]
rs7961626	0.80[EUR][1000 genomes]
rs829017	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs319939	SRSF2IP	cis	parietal	SCAN
rs319939	DDN	cis	cerebellum	SCAN
rs319939	CSRNP2	cis	cerebellum	SCAN
rs319939	LETMD1	Cis_1M	lymphoblastoid	RTeQTL
rs319939	COL2A1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
2	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
4	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
6	chr12:51331800-51353800	Weak transcription	Primary T cells from cord blood	blood
7	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:51331800-51382000	Weak transcription	Ovary	ovary
9	chr12:51332600-51354400	Weak transcription	Thymus	Thymus
10	chr12:51332600-51365000	Weak transcription	Fetal Brain Female	brain
11	chr12:51340000-51361800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:51341400-51348600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
14	chr12:51341800-51372600	Weak transcription	Osteobl	bone
15	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
16	chr12:51342200-51361200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:51342400-51360000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:51342400-51373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:51342800-51346600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:51342800-51378400	Weak transcription	NHLF	lung
21	chr12:51343000-51355400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:51343000-51366200	Weak transcription	Brain Germinal Matrix	brain
23	chr12:51343200-51361600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:51343400-51355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:51343600-51366200	Weak transcription	Gastric	stomach
26	chr12:51344000-51361400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
28	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
29	chr12:51345000-51361200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:51345600-51354000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:51346200-51346600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:51346200-51346600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:51346200-51347000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:51346200-51347000	Strong transcription	Fetal Stomach	stomach
35	chr12:51346200-51347200	Strong transcription	Fetal Muscle Leg	muscle
36	chr12:51346200-51347400	Strong transcription	Brain Anterior Caudate	brain
37	chr12:51346200-51347400	Strong transcription	Fetal Intestine Small	intestine
38	chr12:51346400-51347200	Strong transcription	Brain Angular Gyrus	brain
39	chr12:51346400-51347200	Strong transcription	Brain Hippocampus Middle	brain
40	chr12:51346400-51347200	Strong transcription	Lung	lung
41	chr12:51346400-51347400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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