Variant report

Variant	rs546052
Chromosome Location	chr11:100809838-100809839
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10791434	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10791435	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10791436	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10791437	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10791438	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10895031	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11224535	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1145435	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1217180	0.86[EUR][1000 genomes]
rs1941370	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1941371	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1941372	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2155442	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2155443	0.81[AFR][1000 genomes]
rs2155793	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2510624	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2510625	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2510626	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3017866	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs471180	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs474651	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4753987	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs477567	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs480080	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs481991	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs482050	1.00[CEU][hapmap]
rs483789	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs485767	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs491964	0.91[EUR][1000 genomes]
rs493079	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs494451	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs494907	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs499861	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs501797	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503455	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs504081	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505405	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs506242	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508850	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508950	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs509013	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs509166	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs509676	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs512405	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs513057	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs514101	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs514403	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs515868	0.82[YRI][hapmap];0.92[AFR][1000 genomes]
rs518675	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs519235	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs519594	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs520403	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs520539	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs521216	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs522337	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs522988	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs524416	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs525129	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs525940	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs529194	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs532783	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs534623	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs535518	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs536270	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs538158	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs539204	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs540000	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs540961	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs541056	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs544257	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs544388	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs546059	0.86[EUR][1000 genomes]
rs547105	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs551502	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs552391	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs560235	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs562891	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs563460	0.86[YRI][hapmap]
rs566608	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs571904	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs572838	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs575448	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs575617	0.81[EUR][1000 genomes]
rs576355	0.84[EUR][1000 genomes]
rs576472	0.81[AFR][1000 genomes]
rs577170	0.82[EUR][1000 genomes]
rs577251	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs578102	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs580773	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs583989	0.81[EUR][1000 genomes]
rs584029	0.86[EUR][1000 genomes]
rs594200	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs594985	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs595761	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs602385	1.00[CEU][hapmap]
rs607889	0.89[EUR][1000 genomes]
rs611591	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs616164	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs617898	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs618017	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs618155	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs618907	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs619066	1.00[CEU][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs620790	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs621172	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs626529	0.81[AFR][1000 genomes]
rs629442	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs629677	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs632725	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs633967	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs637508	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs638004	0.89[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs641948	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs649369	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs649394	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs650269	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs652017	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs652559	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs653344	0.84[CEU][hapmap];0.95[EUR][1000 genomes]
rs662173	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs663622	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs673125	0.85[EUR][1000 genomes]
rs676976	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs678351	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs678775	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs688664	0.89[EUR][1000 genomes]
rs693760	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs694078	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs694556	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7929787	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7933457	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7952007	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7952634	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048356	chr11:100713096-101058995	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv541154	chr11:100713096-101058995	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1054453	chr11:100802521-100814626	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv1037830	chr11:100802521-100818129	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv1051139	chr11:100802521-100819447	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv1051291	chr11:100803267-100814626	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100772000-100831400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr11:100774800-100812800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:100785400-100838400	Weak transcription	Fetal Intestine Small	intestine
4	chr11:100790200-100812600	Weak transcription	Stomach Mucosa	stomach
5	chr11:100794400-100812800	Weak transcription	Fetal Stomach	stomach
6	chr11:100797600-100811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:100798600-100811600	Weak transcription	Fetal Lung	lung
8	chr11:100798600-100812800	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:100798600-100826600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:100798600-100828200	Weak transcription	Gastric	stomach
11	chr11:100798800-100811400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:100798800-100832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:100799200-100812800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:100799200-100812800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:100800200-100846600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:100800800-100835800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:100801000-100812000	Weak transcription	Fetal Heart	heart
18	chr11:100801000-100814800	Weak transcription	HSMM	muscle
19	chr11:100801000-100819600	Weak transcription	HSMMtube	muscle
20	chr11:100801000-100823200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:100801000-100832400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:100801000-100835000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:100801400-100812600	Weak transcription	A549	lung
24	chr11:100801400-100833800	Weak transcription	NH-A	brain
25	chr11:100803000-100822600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr11:100803600-100811000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:100804000-100826200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:100804200-100812800	Weak transcription	Psoas Muscle	Psoas
29	chr11:100804800-100811000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:100805400-100812800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:100806600-100837200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:100806800-100811800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:100806800-100832400	Weak transcription	Fetal Intestine Large	intestine
34	chr11:100807800-100844600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:100808000-100811000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:100808000-100831200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:100808000-100832200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:100808000-100846600	Weak transcription	Ovary	ovary
39	chr11:100808400-100810400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:100808600-100810800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:100808800-100810400	Strong transcription	Primary B cells from cord blood	blood
42	chr11:100808800-100811800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:100809200-100812600	Weak transcription	Liver	Liver
44	chr11:100809200-100812800	Weak transcription	Adipose Nuclei	Adipose
45	chr11:100809800-100810000	Enhancers	Left Ventricle	heart
46	chr11:100809800-100810000	Enhancers	Right Atrium	heart
47	chr11:100809800-100810000	Enhancers	Small Intestine	intestine
48	chr11:100809800-100810600	Enhancers	Rectal Smooth Muscle	rectum
49	chr11:100809800-100811200	Enhancers	Fetal Muscle Leg	muscle
50	chr11:100809800-100813000	Weak transcription	Placenta	Placenta

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