Variant report

Variant	rs6483883
Chromosome Location	chr11:10033265-10033266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10128601	0.85[AFR][1000 genomes]
rs10160515	0.81[ASN][1000 genomes]
rs10734652	0.93[ASW][hapmap]
rs10770080	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10770082	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs10770083	0.87[AFR][1000 genomes]
rs10770084	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs10770085	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10770096	0.81[EUR][1000 genomes]
rs10840331	0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10840332	0.86[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10840335	0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10840339	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840342	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840346	1.00[ASW][hapmap];0.88[LWK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs10840349	0.85[AFR][1000 genomes]
rs10840353	0.88[AFR][1000 genomes]
rs10840354	0.89[AFR][1000 genomes]
rs10840357	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs10840358	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10840363	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs11042581	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11042582	0.91[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042583	0.81[ASN][1000 genomes]
rs11042598	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11042617	0.93[ASW][hapmap];0.85[LWK][hapmap]
rs11042622	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs11042638	0.85[AFR][1000 genomes]
rs11600852	0.90[AFR][1000 genomes]
rs12288355	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs12295754	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12360854	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs2403228	0.80[AMR][1000 genomes]
rs2403230	1.00[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2403259	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2403265	0.85[AFR][1000 genomes]
rs2403268	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4284389	0.89[AFR][1000 genomes]
rs4309158	0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4316505	0.89[AFR][1000 genomes]
rs4323860	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs4350354	0.89[AFR][1000 genomes]
rs4635071	0.80[AFR][1000 genomes]
rs4909918	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4910085	0.80[ASW][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap]
rs4910089	0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs4910097	0.96[CEU][hapmap]
rs58623593	0.88[AFR][1000 genomes]
rs6483860	0.89[CHB][hapmap]
rs6483964	0.89[AFR][1000 genomes]
rs6483965	0.85[AFR][1000 genomes]
rs6483966	0.93[ASW][hapmap]
rs6483970	0.87[ASW][hapmap]
rs7102016	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7104821	0.89[AFR][1000 genomes]
rs7106328	0.85[AFR][1000 genomes]
rs7106491	0.90[AFR][1000 genomes]
rs7110312	0.93[ASW][hapmap]
rs7110664	0.89[AFR][1000 genomes]
rs7119000	1.00[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs7120865	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7121704	1.00[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7123728	0.92[CEU][hapmap]
rs7128591	0.88[AFR][1000 genomes]
rs7128698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7129239	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131203	0.85[AFR][1000 genomes]
rs7479039	0.92[CEU][hapmap]
rs7924499	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7928170	0.80[EUR][1000 genomes]
rs7932988	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs7938543	0.92[CEU][hapmap]
rs7939146	0.88[AFR][1000 genomes]
rs7942420	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7947588	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7948166	0.85[AFR][1000 genomes]
rs7950140	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7950240	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv553475	chr11:10019879-10059623	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6483883	OR52B2	cis	parietal	SCAN
rs6483883	OLFML1	cis	cerebellum	SCAN
rs6483883	SYT9	cis	cerebellum	SCAN
rs6483883	ZNF143	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
2	chr11:9985800-10049000	Weak transcription	Left Ventricle	heart
3	chr11:9991200-10060000	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:9994800-10041800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
6	chr11:10004200-10048600	Weak transcription	Brain Angular Gyrus	brain
7	chr11:10007600-10041800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:10010600-10051200	Weak transcription	Ovary	ovary
9	chr11:10012600-10049000	Weak transcription	Fetal Kidney	kidney
10	chr11:10023800-10033400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:10024200-10047800	Weak transcription	Osteobl	bone
12	chr11:10024600-10041600	Weak transcription	HUVEC	blood vessel
13	chr11:10024800-10054000	Weak transcription	Hela-S3	cervix
14	chr11:10030400-10034400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:10030400-10042600	Weak transcription	Fetal Lung	lung
16	chr11:10030600-10033600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:10030600-10047000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:10030600-10051400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:10030600-10054000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:10030600-10065800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:10030800-10033600	Weak transcription	Fetal Stomach	stomach
22	chr11:10030800-10041800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:10031000-10033400	Weak transcription	HSMM	muscle
24	chr11:10031600-10036000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:10032400-10035000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:10032800-10035000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr11:10032800-10035400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr11:10032800-10036000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:10032800-10049200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:10033200-10042400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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