Variant report

Variant	rs7939193
Chromosome Location	chr11:73446369-73446370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1043234	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10501412	1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10736793	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10898943	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898947	0.87[AMR][1000 genomes]
rs10898949	0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
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]
rs11235844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs11235850	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11235851	0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11235852	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11235859	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235860	0.93[EUR][1000 genomes];0.86[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235875	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235881	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235885	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11235886	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235887	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11235888	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11235898	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11235905	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11235907	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11235908	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11235910	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235913	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11235914	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11235915	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235920	0.90[CEU][hapmap];0.91[AMR][1000 genomes]
rs11235922	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11235925	1.00[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11235927	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11235931	0.87[AMR][1000 genomes]
rs11235933	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs11235934	0.87[AMR][1000 genomes]
rs11235937	0.83[CHD][hapmap]
rs11235939	0.87[AMR][1000 genomes]
rs11235947	0.87[AMR][1000 genomes]
rs12274970	0.81[GIH][hapmap]
rs12365044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12365080	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12366033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12420099	0.87[AMR][1000 genomes]
rs12420751	0.87[AMR][1000 genomes]
rs12421077	0.87[AMR][1000 genomes]
rs12421900	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1464908	0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17132369	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17132397	0.87[AMR][1000 genomes]
rs17132403	0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs17132411	0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs1723840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1814547	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1830069	0.97[ASN][1000 genomes]
rs1869433	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2037710	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2067912	0.87[CHD][hapmap]
rs2140892	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3211165	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741137	0.87[AMR][1000 genomes]
rs3741147	0.87[TSI][hapmap]
rs3825003	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]
rs4537782	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4944028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944029	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944034	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4944856	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944868	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944869	0.87[AMR][1000 genomes]
rs55910552	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58862453	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60020777	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60074535	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60239378	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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]
rs6592531	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs66481935	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66556722	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66610247	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66626689	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67167213	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67488767	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68128239	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7105309	0.93[CHB][hapmap];1.00[CHD][hapmap]
rs7106773	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7115166	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119528	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7128512	0.90[JPT][hapmap]
rs72974840	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72974866	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72974869	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72976852	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72982926	0.87[AMR][1000 genomes]
rs72982937	0.87[AMR][1000 genomes]
rs72989228	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7929705	1.00[AMR][1000 genomes];0.91[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	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	nsv897912	chr11:73436008-73477045	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7939193	PAAF1	cis	lymphoblastoid	seeQTL
rs7939193	FLJ11848	cis	multi-tissue	Pritchard
rs7939193	WDR71	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:73396000-73448000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:73400400-73449400	Weak transcription	Psoas Muscle	Psoas
4	chr11:73409600-73447800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:73411000-73447600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr11:73411000-73460000	Weak transcription	Colonic Mucosa	Colon
7	chr11:73413400-73470800	Weak transcription	Esophagus	oesophagus
8	chr11:73413600-73447600	Weak transcription	Left Ventricle	heart
9	chr11:73415000-73470200	Weak transcription	Aorta	Aorta
10	chr11:73417200-73469600	Weak transcription	Fetal Kidney	kidney
11	chr11:73418400-73463200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:73422400-73454000	Weak transcription	Gastric	stomach
13	chr11:73422800-73448000	Weak transcription	Fetal Brain Female	brain
14	chr11:73428400-73469800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:73430000-73450400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:73430000-73451600	Weak transcription	HSMMtube	muscle
17	chr11:73430000-73460800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:73430200-73448000	Weak transcription	Lung	lung
19	chr11:73430600-73446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:73430600-73446400	Weak transcription	NH-A	brain
21	chr11:73430600-73456800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:73430600-73460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:73430600-73462800	Weak transcription	HMEC	breast
24	chr11:73430600-73468800	Weak transcription	NHLF	lung
25	chr11:73430800-73470600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:73431200-73447800	Weak transcription	Adipose Nuclei	Adipose
27	chr11:73432000-73460600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:73432000-73460600	Weak transcription	Placenta	Placenta
29	chr11:73432000-73462200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:73432000-73465200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr11:73432000-73465200	Weak transcription	NHEK	skin
32	chr11:73432600-73453400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:73435400-73448200	Weak transcription	Hela-S3	cervix
34	chr11:73436600-73460600	Weak transcription	Small Intestine	intestine
35	chr11:73436800-73458600	Weak transcription	K562	blood
36	chr11:73436800-73458800	Weak transcription	A549	lung
37	chr11:73436800-73461000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:73437000-73451000	Weak transcription	Liver	Liver
39	chr11:73437000-73461000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:73437000-73469400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:73437600-73468600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:73441000-73446800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:73441000-73447800	Weak transcription	HepG2	liver
44	chr11:73441000-73458800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:73441200-73447400	Weak transcription	Fetal Intestine Large	intestine
46	chr11:73441200-73447600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:73441200-73447600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr11:73441200-73447600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:73441200-73448000	Weak transcription	Primary T cells from cord blood	blood
50	chr11:73441200-73448400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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