Variant report

Variant	rs2403264
Chromosome Location	chr11:10065453-10065454
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10128601	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10734652	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs10770082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770083	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10770085	0.83[ASN][1000 genomes]
rs10770087	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10770088	0.86[EUR][1000 genomes]
rs10770089	0.89[EUR][1000 genomes]
rs10770090	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10840342	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs10840346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840349	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840353	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840354	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840360	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10840363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs10840365	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840369	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[EUR][1000 genomes]
rs11042582	0.83[CHB][hapmap]
rs11042583	0.82[AMR][1000 genomes]
rs11042598	0.93[ASN][1000 genomes]
rs11042602	0.92[EUR][1000 genomes]
rs11042617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042620	0.86[EUR][1000 genomes]
rs11042621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042625	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042633	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs11042638	0.95[EUR][1000 genomes]
rs11600852	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12224149	0.81[ASN][1000 genomes]
rs12288355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12360854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2403265	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403268	0.84[AFR][1000 genomes]
rs2403290	0.88[EUR][1000 genomes]
rs4284389	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4316505	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4350354	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4366476	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4466825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4509749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4635071	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910085	0.82[YRI][hapmap]
rs4910097	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs58623593	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6483964	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6483965	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6483966	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6483970	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7102016	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7104821	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7106328	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7106491	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7107021	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7110312	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs7110664	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7111072	0.86[EUR][1000 genomes]
rs7119000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7121704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7122422	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7125593	0.93[EUR][1000 genomes]
rs7126376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128591	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131203	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7928170	1.00[CHB][hapmap]
rs7932988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7938891	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7939146	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7947588	0.80[ASN][1000 genomes]
rs7948166	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7950140	0.95[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7950240	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9645625	0.95[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2403264	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
2	chr11:10030600-10065800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:10035200-10065800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:10040400-10065800	Weak transcription	HSMM	muscle
5	chr11:10042200-10066000	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:10042200-10066000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:10042200-10066200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:10042600-10066000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:10043400-10065600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:10043800-10065600	Weak transcription	HepG2	liver
11	chr11:10046400-10065800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:10046400-10065800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:10049400-10065600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:10049800-10065600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:10049800-10066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:10049800-10066000	Weak transcription	Fetal Kidney	kidney
17	chr11:10050200-10066000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:10050200-10066800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:10056200-10066000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:10061600-10066200	Weak transcription	Osteobl	bone
21	chr11:10061800-10066000	Weak transcription	Hela-S3	cervix
22	chr11:10061800-10066200	Weak transcription	NHLF	lung
23	chr11:10063800-10065800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:10063800-10066200	Weak transcription	Fetal Lung	lung
25	chr11:10064000-10065600	Weak transcription	Adipose Nuclei	Adipose
26	chr11:10064200-10066200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:10064800-10066000	Weak transcription	NHDF-Ad	bronchial
28	chr11:10065000-10065800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr11:10065000-10065800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr11:10065000-10066000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:10065000-10066600	ZNF genes & repeats	Dnd41	blood
32	chr11:10065000-10067000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:10065200-10066000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:10065200-10067800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:10065400-10065600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:10065400-10066000	Enhancers	Liver	Liver
37	chr11:10065400-10066800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr11:10065400-10067000	ZNF genes & repeats	A549	lung

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