Variant report

Variant	rs3212430
Chromosome Location	chr5:52325775-52325776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10041086	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10069239	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2075614	0.91[ASN][1000 genomes]
rs2287950	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3212433	0.80[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212435	1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3212436	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212446	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212483	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3212537	0.89[ASN][1000 genomes]
rs3212556	0.88[ASN][1000 genomes]
rs3212583	0.86[YRI][hapmap]
rs3776788	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776789	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3797494	0.93[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797497	0.80[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797500	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357234	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3212430	MOCS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52328600	Weak transcription	Lung	lung
3	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:52314400-52326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:52317200-52327200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:52317400-52326800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:52317600-52326800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
9	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:52318800-52327200	Genic enhancers	HMEC	breast
11	chr5:52319200-52326200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:52319200-52327600	Weak transcription	Fetal Intestine Large	intestine
13	chr5:52319600-52326600	Weak transcription	Small Intestine	intestine
14	chr5:52320600-52326200	Weak transcription	Esophagus	oesophagus
15	chr5:52320600-52327400	Weak transcription	HSMM	muscle
16	chr5:52320600-52327600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:52321000-52326600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:52321600-52326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:52321800-52326000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:52321800-52326800	Weak transcription	Fetal Lung	lung
21	chr5:52322200-52326400	Genic enhancers	HepG2	liver
22	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
23	chr5:52322600-52326400	Weak transcription	Fetal Kidney	kidney
24	chr5:52323000-52326400	Genic enhancers	Hela-S3	cervix
25	chr5:52323000-52327000	Enhancers	A549	lung
26	chr5:52323000-52327200	Genic enhancers	NHEK	skin
27	chr5:52323200-52326400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:52323200-52326400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:52323200-52327000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:52323200-52329000	Enhancers	NHLF	lung
31	chr5:52323400-52325800	Enhancers	Osteobl	bone
32	chr5:52323600-52326200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:52323600-52326200	Enhancers	NHDF-Ad	bronchial
34	chr5:52323600-52332600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:52323800-52326200	Weak transcription	Pancreas	Pancrea
36	chr5:52324200-52326600	Weak transcription	Stomach Mucosa	stomach
37	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
38	chr5:52324400-52326400	Weak transcription	Dnd41	blood
39	chr5:52324400-52326800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:52324400-52327000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:52324400-52327200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:52324400-52327400	Weak transcription	Brain Angular Gyrus	brain
43	chr5:52324400-52328800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
45	chr5:52324600-52326800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:52324600-52327000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:52324600-52332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:52324800-52325800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:52324800-52326200	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:52324800-52326200	Weak transcription	NH-A	brain

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