Variant report

Variant	rs499861
Chromosome Location	chr11:100862593-100862594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10791434	0.88[EUR][1000 genomes]
rs10791435	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10791436	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10791437	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10791438	0.91[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10895031	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11224535	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1145435	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1941370	0.86[EUR][1000 genomes]
rs1941371	0.86[EUR][1000 genomes]
rs1941372	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2020876	1.00[CHD][hapmap]
rs2155442	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2155793	0.86[EUR][1000 genomes]
rs2510624	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2510625	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2510626	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3017866	0.86[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs471180	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs474651	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4753987	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs477567	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs480080	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs481991	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs482050	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs483789	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs485767	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs491964	0.87[EUR][1000 genomes]
rs493079	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs494451	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs494907	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs501797	0.91[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs503455	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs504081	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs505405	0.89[CEU][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs506242	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs508850	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs508950	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs509013	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs509166	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs509676	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs512405	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs513057	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs514101	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs514403	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs518675	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs519235	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs519594	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs520403	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs520539	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs521216	0.90[EUR][1000 genomes]
rs522337	0.90[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs522988	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs524416	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs525129	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs525940	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs529194	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs532783	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs534623	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs535518	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs536270	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs538158	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs539204	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs540000	0.91[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs540961	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs541056	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs544257	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs544388	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs546052	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs547105	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs551502	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs552391	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs560235	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs562891	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs563460	0.81[MKK][hapmap]
rs566608	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs571904	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs572838	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs575448	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs575617	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs576355	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs577251	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs578102	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs580773	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs594200	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs594985	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs595761	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs602385	0.85[CEU][hapmap]
rs616164	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs617898	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs618017	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs618155	0.91[CEU][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs618907	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs619066	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs620790	0.91[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs621172	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs629677	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap]
rs632725	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs633967	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs637508	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs638004	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs641948	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap]
rs649369	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs649394	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs650269	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs652017	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs652559	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs653344	1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs662173	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs663622	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs673125	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs676976	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678351	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678775	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs693760	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs694078	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694556	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7929787	0.85[EUR][1000 genomes]
rs7933457	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7952007	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7952634	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs499861	PGR	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100844800-100863000	Weak transcription	Brain Anterior Caudate	brain
2	chr11:100848200-100866000	Weak transcription	Psoas Muscle	Psoas
3	chr11:100848400-100863200	Weak transcription	Fetal Intestine Large	intestine
4	chr11:100848400-100864600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:100848600-100863400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:100848600-100865200	Weak transcription	Left Ventricle	heart
7	chr11:100848600-100865800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:100848800-100864800	Weak transcription	HSMM	muscle
9	chr11:100849000-100863000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:100849200-100867400	Weak transcription	Fetal Lung	lung
11	chr11:100850600-100864600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:100851000-100870400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:100856400-100862600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:100857400-100864600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:100857600-100870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:100858600-100862800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:100858600-100865600	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:100858600-100870400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:100859200-100862600	Strong transcription	Liver	Liver
20	chr11:100860000-100864600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:100861600-100862600	Strong transcription	Adipose Nuclei	Adipose
22	chr11:100861600-100864000	Enhancers	Primary T cells from cord blood	blood
23	chr11:100861800-100862600	Enhancers	Aorta	Aorta
24	chr11:100861800-100866000	Weak transcription	HSMMtube	muscle
25	chr11:100862000-100863000	Active TSS	Ovary	ovary
26	chr11:100862000-100863800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:100862200-100862600	Enhancers	Dnd41	blood
28	chr11:100862400-100865600	Weak transcription	Placenta	Placenta
29	chr11:100862400-100866800	Weak transcription	Fetal Heart	heart

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