Variant report

Variant	rs10047442
Chromosome Location	chr11:73186864-73186865
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1002126	0.87[CEU][hapmap]
rs10793060	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10898920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898925	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11235729	0.84[EUR][1000 genomes]
rs11235743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11235746	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11820786	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11820929	1.00[CHB][hapmap]
rs11821094	0.85[CHB][hapmap]
rs11823923	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs11824614	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs11826896	0.83[CEU][hapmap];0.95[GIH][hapmap];0.96[YRI][hapmap]
rs11826909	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs12275766	0.85[CHB][hapmap]
rs12276536	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12282282	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs12295744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12421053	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs1894076	0.85[CHB][hapmap]
rs1939382	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027761	0.85[CHB][hapmap]
rs2027763	0.85[CHB][hapmap]
rs2298807	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs2366780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741148	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3741149	0.85[CHB][hapmap]
rs4944845	0.86[ASN][1000 genomes]
rs55751428	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56801796	0.83[EUR][1000 genomes]
rs6592521	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs6592523	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7101831	0.83[CEU][hapmap];0.96[YRI][hapmap]
rs7114009	0.85[MKK][hapmap];0.96[YRI][hapmap]
rs7119167	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7122560	0.84[EUR][1000 genomes]
rs7127171	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131383	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs725103	0.85[CHB][hapmap]
rs7342205	0.85[CHB][hapmap]
rs73542998	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7925573	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930880	0.85[CHB][hapmap]
rs7935204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7937066	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7944099	0.85[CHB][hapmap]
rs7945596	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7948630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs7950002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7952686	1.00[CEU][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs876480	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs880317	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs947837	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv508641	chr11:73149281-73235528	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv520130	chr11:73183598-73223776	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10047442	ARHGEF17	cis	multi-tissue	Pritchard
rs10047442	ANO1	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73123800-73209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:73131000-73190000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr11:73141800-73231600	Weak transcription	Thymus	Thymus
4	chr11:73151000-73187000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:73156000-73187800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:73163800-73225600	Weak transcription	Fetal Stomach	stomach
7	chr11:73168600-73189800	Weak transcription	Hela-S3	cervix
8	chr11:73172800-73218800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:73174600-73187800	Weak transcription	Primary T cells from cord blood	blood
10	chr11:73177000-73189800	Weak transcription	Fetal Heart	heart
11	chr11:73177400-73189800	Weak transcription	HMEC	breast
12	chr11:73177400-73190000	Weak transcription	Osteobl	bone
13	chr11:73177400-73191400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:73177400-73191800	Weak transcription	NHDF-Ad	bronchial
15	chr11:73178600-73190000	Weak transcription	Fetal Brain Male	brain
16	chr11:73179600-73192400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:73180000-73188000	Weak transcription	Primary B cells from cord blood	blood
18	chr11:73180000-73191800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:73180600-73189600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:73181600-73188000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:73181600-73189800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:73182000-73230000	Weak transcription	Dnd41	blood
23	chr11:73182200-73189400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:73185800-73187000	Enhancers	Psoas Muscle	Psoas
25	chr11:73186000-73187200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr11:73186200-73187200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr11:73186200-73205200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:73186600-73187000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:73186600-73187000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr11:73186600-73187200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:73186600-73187200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:73186800-73187000	Enhancers	Brain Substantia Nigra	brain
33	chr11:73186800-73187000	Enhancers	Left Ventricle	heart
34	chr11:73186800-73187000	Enhancers	Right Atrium	heart
35	chr11:73186800-73187000	Enhancers	Right Ventricle	heart
36	chr11:73186800-73187200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr11:73186800-73187200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:73186800-73187200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:73186800-73187200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:73186800-73187200	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr11:73186800-73187200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr11:73186800-73187200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr11:73186800-73187200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:73186800-73187400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr11:73186800-73187400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr11:73186800-73187400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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