Variant report

Variant	rs3825003
Chromosome Location	chr11:73389112-73389113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73385994..73387956-chr11:73388947..73391693,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1043234	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10501412	1.00[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs10736793	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10898943	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10898949	0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs11235834	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs11235843	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11235850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235851	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235852	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11235859	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235860	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235864	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235875	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235881	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235882	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11235886	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11235888	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11235898	0.84[EUR][1000 genomes]
rs11235905	0.83[EUR][1000 genomes]
rs11235907	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs11235908	1.00[CEU][hapmap]
rs11235920	0.90[CEU][hapmap]
rs11235922	1.00[CEU][hapmap]
rs11235925	1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs11235927	1.00[CEU][hapmap]
rs11235933	1.00[MEX][hapmap]
rs12274970	0.81[GIH][hapmap]
rs12365044	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12365080	1.00[CEU][hapmap]
rs12366033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1464908	0.89[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs17132369	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17132403	0.88[JPT][hapmap]
rs17132411	0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs1723840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1830069	0.86[ASN][1000 genomes]
rs1869433	1.00[CEU][hapmap]
rs2037710	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2140892	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272248	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3211165	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741147	0.87[TSI][hapmap]
rs4944028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944029	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944033	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4944034	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4944852	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4944856	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944862	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60020777	0.83[EUR][1000 genomes]
rs60074535	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60239378	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6590	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6592531	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs66481935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66556722	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66610247	0.83[EUR][1000 genomes]
rs66626689	0.82[EUR][1000 genomes]
rs67167213	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67488767	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68128239	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105309	0.93[CHB][hapmap];1.00[CHD][hapmap]
rs7106773	0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs7115166	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7119528	1.00[CEU][hapmap]
rs7128512	0.90[JPT][hapmap]
rs72974833	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72974840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72974866	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72974869	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72976852	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7939193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][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	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	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv390	chr11:73388188-73432899	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3825003	PAAF1	cis	lymphoblastoid	seeQTL
rs3825003	WDR71	cis	multi-tissue	Pritchard
rs3825003	FLJ11848	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73372400-73395400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:73372600-73394800	Weak transcription	Brain Germinal Matrix	brain
3	chr11:73372800-73390600	Weak transcription	HUVEC	blood vessel
4	chr11:73374200-73391800	Weak transcription	Hela-S3	cervix
5	chr11:73374400-73427200	Weak transcription	A549	lung
6	chr11:73375200-73404400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:73375800-73400000	Weak transcription	Lung	lung
8	chr11:73375800-73416200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:73376200-73390400	Weak transcription	Brain Anterior Caudate	brain
10	chr11:73376200-73395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:73376200-73398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:73376600-73399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:73376600-73400000	Weak transcription	Spleen	Spleen
14	chr11:73377000-73400000	Weak transcription	Psoas Muscle	Psoas
15	chr11:73381800-73400000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:73382200-73399000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:73382200-73436000	Weak transcription	Small Intestine	intestine
18	chr11:73382200-73441200	Weak transcription	Stomach Mucosa	stomach
19	chr11:73382400-73421600	Weak transcription	Gastric	stomach
20	chr11:73382800-73400400	Weak transcription	Pancreas	Pancrea
21	chr11:73383200-73399000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:73383400-73427200	Weak transcription	Fetal Heart	heart
23	chr11:73383800-73395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:73384000-73427600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:73384800-73401800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:73385200-73389800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:73385200-73391000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:73385200-73391200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:73385200-73392000	Strong transcription	Placenta	Placenta
31	chr11:73385200-73393600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:73385400-73390400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:73385600-73395400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:73385600-73398800	Weak transcription	Aorta	Aorta
35	chr11:73385800-73389200	Weak transcription	Fetal Intestine Small	intestine
36	chr11:73385800-73411400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:73386200-73392400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:73386400-73390000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:73386400-73390200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:73386400-73395200	Weak transcription	Thymus	Thymus
41	chr11:73386400-73397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr11:73386600-73399400	Weak transcription	Esophagus	oesophagus
43	chr11:73386800-73399400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:73387000-73393000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:73387000-73395200	Weak transcription	Ovary	ovary
46	chr11:73387400-73389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:73387400-73410800	Weak transcription	Colonic Mucosa	Colon
48	chr11:73387600-73389400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr11:73387600-73390800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:73387600-73390800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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