Variant report

Variant	rs10038285
Chromosome Location	chr5:42689540-42689541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10038477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10041108	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs10041130	0.90[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.91[EUR][1000 genomes]
rs10044169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10050889	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs10061833	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10063672	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10074740	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10077296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10473288	0.85[EUR][1000 genomes]
rs10805665	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10941583	0.90[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10941588	0.84[EUR][1000 genomes]
rs1109882	0.85[EUR][1000 genomes]
rs12513710	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12514437	0.85[EUR][1000 genomes]
rs12518067	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs12521311	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12652476	0.89[JPT][hapmap]
rs12654861	0.89[JPT][hapmap]
rs1423655	0.90[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs16872680	0.88[JPT][hapmap]
rs16872694	0.89[JPT][hapmap]
rs16872762	0.89[JPT][hapmap]
rs16872777	0.89[JPT][hapmap]
rs16872791	0.89[JPT][hapmap]
rs230808	0.85[EUR][1000 genomes]
rs230811	0.85[EUR][1000 genomes]
rs28551699	0.82[EUR][1000 genomes]
rs28919903	0.88[JPT][hapmap]
rs28919913	0.82[EUR][1000 genomes]
rs2910854	0.86[EUR][1000 genomes]
rs2910860	0.90[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs2910863	0.86[EUR][1000 genomes]
rs2910866	0.86[EUR][1000 genomes]
rs2910878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2910879	0.89[JPT][hapmap]
rs2972780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972991	0.89[JPT][hapmap]
rs2973004	0.88[JPT][hapmap]
rs2973008	0.86[EUR][1000 genomes]
rs34159518	0.84[EUR][1000 genomes]
rs35291899	0.88[ASN][1000 genomes]
rs3877899	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs3884519	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4073475	0.82[EUR][1000 genomes]
rs4073476	0.82[EUR][1000 genomes]
rs4146624	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4242116	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs4242117	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4242118	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4242119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4242122	0.86[EUR][1000 genomes]
rs4242123	0.86[EUR][1000 genomes]
rs4242124	0.85[EUR][1000 genomes]
rs4273617	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4315928	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4357041	0.82[EUR][1000 genomes]
rs4357043	0.95[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs4376276	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4394131	0.94[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4518410	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4523006	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4547964	0.93[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4569879	0.85[EUR][1000 genomes]
rs4590183	0.95[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4610468	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4612114	0.84[EUR][1000 genomes]
rs4637559	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4866793	0.85[EUR][1000 genomes]
rs4866947	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4866948	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4866955	0.86[EUR][1000 genomes]
rs4866956	0.84[EUR][1000 genomes]
rs4866957	0.84[EUR][1000 genomes]
rs56350930	0.83[EUR][1000 genomes]
rs6179	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6182	0.89[JPT][hapmap]
rs6184	0.89[JPT][hapmap]
rs6413428	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6414898	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs6451627	0.94[ASW][hapmap];0.95[CEU][hapmap];0.83[CHD][hapmap];0.80[MKK][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6451641	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs6451643	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6864999	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6871947	0.85[EUR][1000 genomes]
rs6873340	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs6873545	0.95[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs6886047	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6897530	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7442754	0.86[EUR][1000 genomes]
rs7444761	0.80[CEU][hapmap];0.89[EUR][1000 genomes]
rs7447061	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7701605	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs7703289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7715032	0.90[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1019648	chr5:42616487-42696943	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv537736	chr5:42616487-42696943	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10038285	CARD6	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42677000-42691600	Weak transcription	Aorta	Aorta
2	chr5:42679800-42691600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:42683200-42691200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:42685000-42691800	Weak transcription	Right Ventricle	heart
5	chr5:42685400-42691200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:42687000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:42687200-42689800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:42687400-42691800	Weak transcription	Gastric	stomach
9	chr5:42687800-42700600	Weak transcription	Fetal Intestine Large	intestine
10	chr5:42688000-42691600	Weak transcription	Ovary	ovary
11	chr5:42688000-42692200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:42688000-42699800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:42688200-42691200	Weak transcription	Fetal Stomach	stomach
14	chr5:42688400-42689600	Weak transcription	Fetal Heart	heart
15	chr5:42688400-42689600	Strong transcription	Left Ventricle	heart
16	chr5:42688400-42690400	Strong transcription	Fetal Muscle Leg	muscle
17	chr5:42688400-42722200	Weak transcription	Pancreas	Pancrea
18	chr5:42688600-42699000	Weak transcription	Esophagus	oesophagus
19	chr5:42688800-42690400	Strong transcription	Fetal Lung	lung
20	chr5:42689000-42690400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:42689000-42690600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:42689200-42689800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:42689200-42690400	Enhancers	Psoas Muscle	Psoas
24	chr5:42689400-42689600	Active TSS	Spleen	Spleen
25	chr5:42689400-42689800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:42689400-42689800	Genic enhancers	Adipose Nuclei	Adipose
27	chr5:42689400-42689800	Genic enhancers	Liver	Liver
28	chr5:42689400-42690200	Weak transcription	Placenta	Placenta
29	chr5:42689400-42690400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:42689400-42690400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:42689400-42690400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:42689400-42690400	Enhancers	Right Atrium	heart
33	chr5:42689400-42691800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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