Variant report

Variant	rs4273617
Chromosome Location	chr5:42695471-42695472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10038285	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]
rs10038477	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10041108	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs10041130	0.90[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10044169	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10050889	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10061833	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10074740	0.89[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10077296	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10805665	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10941583	0.90[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10941588	0.80[EUR][1000 genomes]
rs1109882	0.82[EUR][1000 genomes]
rs12514437	0.82[EUR][1000 genomes]
rs12518067	0.88[ASW][hapmap];1.00[CEU][hapmap]
rs12521311	0.82[EUR][1000 genomes]
rs12652476	0.89[JPT][hapmap]
rs12654861	0.89[JPT][hapmap]
rs13153760	0.80[EUR][1000 genomes]
rs13153784	0.80[EUR][1000 genomes]
rs13154178	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs1345824	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs1423655	0.90[CEU][hapmap];0.89[JPT][hapmap];0.83[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	0.82[EUR][1000 genomes]
rs230811	0.82[EUR][1000 genomes]
rs28919903	0.88[JPT][hapmap]
rs2910854	0.83[EUR][1000 genomes]
rs2910860	0.90[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2910863	0.83[EUR][1000 genomes]
rs2910866	0.83[EUR][1000 genomes]
rs2910875	0.98[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap]
rs2910878	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2910879	0.89[JPT][hapmap]
rs2972780	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972991	0.89[JPT][hapmap]
rs2973004	0.88[JPT][hapmap]
rs2973008	0.83[EUR][1000 genomes]
rs2973015	0.89[YRI][hapmap]
rs2973018	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs34159518	0.80[EUR][1000 genomes]
rs35291899	0.89[ASN][1000 genomes]
rs3877899	0.85[CEU][hapmap]
rs4146624	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4242116	0.88[ASW][hapmap];1.00[CEU][hapmap]
rs4242117	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs4242118	0.80[EUR][1000 genomes]
rs4242119	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4242122	0.83[EUR][1000 genomes]
rs4242123	0.83[EUR][1000 genomes]
rs4242124	0.82[EUR][1000 genomes]
rs4315928	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4357043	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs4376276	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4394131	0.88[ASW][hapmap];0.95[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs4547964	0.93[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4569879	0.81[EUR][1000 genomes]
rs4590183	0.95[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs4637559	0.89[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4866793	0.82[EUR][1000 genomes]
rs4866947	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4866948	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4866955	0.83[EUR][1000 genomes]
rs6179	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6180	0.86[YRI][hapmap]
rs6182	0.89[JPT][hapmap]
rs6184	0.89[JPT][hapmap]
rs6413428	0.90[CEU][hapmap]
rs6414898	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs6451627	0.88[ASW][hapmap];0.95[CEU][hapmap]
rs6451641	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6451643	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6864999	0.81[EUR][1000 genomes]
rs6871947	0.82[EUR][1000 genomes]
rs6873340	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6873545	0.95[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs6886047	0.95[CEU][hapmap]
rs6897530	0.82[EUR][1000 genomes]
rs7442754	0.83[EUR][1000 genomes]
rs7444761	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs7447061	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7701605	0.88[ASW][hapmap];1.00[CEU][hapmap]
rs7703289	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7715032	0.90[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]

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
rs4273617	CARD6	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42687800-42700600	Weak transcription	Fetal Intestine Large	intestine
2	chr5:42688000-42699800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:42688400-42722200	Weak transcription	Pancreas	Pancrea
4	chr5:42688600-42699000	Weak transcription	Esophagus	oesophagus
5	chr5:42689800-42703000	Strong transcription	Liver	Liver
6	chr5:42689800-42703400	Strong transcription	Adipose Nuclei	Adipose
7	chr5:42690400-42700000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:42690400-42701200	Weak transcription	Fetal Lung	lung
9	chr5:42692200-42696800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:42692200-42697400	Weak transcription	Left Ventricle	heart
11	chr5:42692200-42697400	Weak transcription	Ovary	ovary
12	chr5:42692200-42700800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:42692200-42703000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:42692200-42703200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:42692200-42703200	Weak transcription	Right Ventricle	heart
16	chr5:42692200-42705600	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:42692400-42705600	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:42692600-42697400	Weak transcription	Fetal Stomach	stomach
19	chr5:42692600-42698000	Weak transcription	Fetal Heart	heart
20	chr5:42692600-42702800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:42693000-42699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:42694000-42695800	Weak transcription	Spleen	Spleen
23	chr5:42694000-42696200	Weak transcription	Aorta	Aorta
24	chr5:42694000-42697800	Weak transcription	Psoas Muscle	Psoas
25	chr5:42694600-42696400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:42695400-42699200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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