Variant report

Variant	rs6592531
Chromosome Location	chr11:73412354-73412355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1043234	0.86[ASN][1000 genomes]
rs10501412	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs10736793	0.93[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];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898943	0.83[ASN][1000 genomes]
rs10898949	0.84[CHD][hapmap]
rs11235834	0.81[JPT][hapmap]
rs11235843	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs11235844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11235850	0.94[ASN][1000 genomes]
rs11235851	0.86[CHB][hapmap];0.84[CHD][hapmap];0.97[ASN][1000 genomes]
rs11235852	0.96[ASN][1000 genomes]
rs11235859	1.00[ASN][1000 genomes]
rs11235860	1.00[ASN][1000 genomes]
rs11235864	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235875	0.88[ASN][1000 genomes]
rs11235881	0.88[ASN][1000 genomes]
rs11235882	0.86[ASN][1000 genomes]
rs11235886	0.83[ASN][1000 genomes]
rs11235888	0.86[ASN][1000 genomes]
rs11235907	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs11235925	0.84[CHD][hapmap];0.82[GIH][hapmap]
rs12365044	0.83[ASN][1000 genomes]
rs12366033	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464908	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17132369	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs17132403	0.88[JPT][hapmap]
rs17132411	0.84[CHD][hapmap]
rs1723840	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1830069	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2037710	1.00[ASN][1000 genomes]
rs2067912	0.84[CHD][hapmap]
rs2140892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[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];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3211165	0.86[ASN][1000 genomes]
rs3825003	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4944028	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4944029	1.00[ASN][1000 genomes]
rs4944032	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4944033	0.86[ASN][1000 genomes]
rs4944856	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4944862	0.86[ASN][1000 genomes]
rs58862453	0.80[ASN][1000 genomes]
rs60074535	0.86[ASN][1000 genomes]
rs60239378	0.83[ASN][1000 genomes]
rs6590	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs66481935	0.94[ASN][1000 genomes]
rs66556722	1.00[ASN][1000 genomes]
rs66626689	0.80[ASN][1000 genomes]
rs67167213	0.88[ASN][1000 genomes]
rs67488767	0.88[ASN][1000 genomes]
rs68128239	1.00[ASN][1000 genomes]
rs7101957	0.87[YRI][hapmap]
rs7105309	0.93[CHB][hapmap];1.00[CHD][hapmap]
rs7106773	0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7115166	0.88[ASN][1000 genomes]
rs7128512	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs72974833	0.81[ASN][1000 genomes]
rs72974840	0.94[ASN][1000 genomes]
rs72974866	1.00[ASN][1000 genomes]
rs72974869	0.94[ASN][1000 genomes]
rs72976852	0.88[ASN][1000 genomes]
rs7939193	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv975363	chr11:73411321-73426936	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6592531	PAAF1	cis	lymphoblastoid	seeQTL
rs6592531	FLJ11848	cis	multi-tissue	Pritchard
rs6592531	KRTAP5-11	cis	cerebellum	SCAN
rs6592531	GDPD4	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73374400-73427200	Weak transcription	A549	lung
2	chr11:73375800-73416200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:73382200-73436000	Weak transcription	Small Intestine	intestine
4	chr11:73382200-73441200	Weak transcription	Stomach Mucosa	stomach
5	chr11:73382400-73421600	Weak transcription	Gastric	stomach
6	chr11:73383400-73427200	Weak transcription	Fetal Heart	heart
7	chr11:73384000-73427600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:73389000-73445400	Weak transcription	Fetal Brain Male	brain
10	chr11:73389200-73416800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:73389200-73427400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:73389200-73440200	Weak transcription	Right Ventricle	heart
13	chr11:73390800-73429600	Weak transcription	NHLF	lung
14	chr11:73391000-73433600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:73394400-73430200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:73395600-73416200	Weak transcription	Brain Anterior Caudate	brain
17	chr11:73395800-73412600	Weak transcription	Thymus	Thymus
18	chr11:73396000-73448000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:73397800-73426600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:73399000-73412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:73399600-73412400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:73400000-73416200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:73400200-73414600	Weak transcription	Ovary	ovary
24	chr11:73400400-73449400	Weak transcription	Psoas Muscle	Psoas
25	chr11:73400600-73412600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:73400600-73412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:73400600-73412800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:73400600-73412800	Weak transcription	Aorta	Aorta
29	chr11:73400600-73421600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:73400800-73416200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:73400800-73422000	Weak transcription	Spleen	Spleen
32	chr11:73401000-73412600	Weak transcription	Esophagus	oesophagus
33	chr11:73401000-73412800	Weak transcription	HUVEC	blood vessel
34	chr11:73401000-73416400	Weak transcription	Fetal Kidney	kidney
35	chr11:73402000-73422200	Weak transcription	Hela-S3	cervix
36	chr11:73402600-73412600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:73404400-73420200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:73404400-73424200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:73404400-73427400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:73404800-73420400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:73405000-73412800	Weak transcription	Lung	lung
42	chr11:73405000-73421800	Weak transcription	Pancreas	Pancrea
43	chr11:73405200-73414400	Weak transcription	Brain Germinal Matrix	brain
44	chr11:73405200-73416200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:73405200-73416800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:73405200-73429600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:73405400-73416800	Weak transcription	K562	blood
48	chr11:73405400-73422000	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:73405400-73426400	Weak transcription	Brain Substantia Nigra	brain
50	chr11:73405800-73412600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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