Variant report

Variant	rs2140892
Chromosome Location	chr11:73422879-73422880
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	chr11:73422546..73424731-chr11:73470843..73472960,2	K562	blood:
2	chr11:73421710..73424009-chr11:73461398..73464221,2	K562	blood:

Variant related genes	Relation type
ENSG00000175582	Chromatin interaction
ENSG00000256034	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1043234	0.97[ASN][1000 genomes]
rs10501412	0.82[GIH][hapmap]
rs10736793	0.93[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];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898943	0.94[ASN][1000 genomes]
rs11235834	0.81[JPT][hapmap]
rs11235843	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs11235844	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11235850	0.83[ASN][1000 genomes]
rs11235851	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs11235852	0.87[ASN][1000 genomes]
rs11235859	0.88[ASN][1000 genomes]
rs11235860	0.88[ASN][1000 genomes]
rs11235864	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11235875	1.00[ASN][1000 genomes]
rs11235881	1.00[ASN][1000 genomes]
rs11235882	0.97[ASN][1000 genomes]
rs11235885	0.88[ASN][1000 genomes]
rs11235886	0.94[ASN][1000 genomes]
rs11235887	0.90[ASN][1000 genomes]
rs11235888	0.97[ASN][1000 genomes]
rs11235898	0.81[ASN][1000 genomes]
rs11235905	0.81[ASN][1000 genomes]
rs11235907	0.96[CHD][hapmap];0.92[GIH][hapmap];0.81[ASN][1000 genomes]
rs11235908	0.81[ASN][1000 genomes]
rs11235910	0.81[ASN][1000 genomes]
rs11235913	0.81[ASN][1000 genomes]
rs11235914	0.81[ASN][1000 genomes]
rs11235915	0.81[ASN][1000 genomes]
rs11235925	0.82[GIH][hapmap]
rs12365044	0.94[ASN][1000 genomes]
rs12366033	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1464908	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17132369	0.96[CHD][hapmap];0.92[GIH][hapmap];0.81[ASN][1000 genomes]
rs17132403	0.88[JPT][hapmap]
rs1723840	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1830069	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037710	0.88[ASN][1000 genomes]
rs3211165	0.97[ASN][1000 genomes]
rs3825003	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4944028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4944029	0.88[ASN][1000 genomes]
rs4944032	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4944033	0.97[ASN][1000 genomes]
rs4944034	0.81[ASN][1000 genomes]
rs4944856	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4944862	0.97[ASN][1000 genomes]
rs55910552	0.81[ASN][1000 genomes]
rs58862453	0.89[ASN][1000 genomes]
rs60020777	0.81[ASN][1000 genomes]
rs60074535	0.97[ASN][1000 genomes]
rs60239378	0.91[ASN][1000 genomes]
rs6590	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs6592531	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]
rs66481935	0.83[ASN][1000 genomes]
rs66556722	0.88[ASN][1000 genomes]
rs66610247	0.81[ASN][1000 genomes]
rs66626689	0.91[ASN][1000 genomes]
rs67167213	1.00[ASN][1000 genomes]
rs67488767	1.00[ASN][1000 genomes]
rs68128239	0.88[ASN][1000 genomes]
rs7101957	0.87[YRI][hapmap]
rs7105309	0.93[CHB][hapmap];0.96[CHD][hapmap]
rs7106773	0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7115166	1.00[ASN][1000 genomes]
rs7128512	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs72974840	0.83[ASN][1000 genomes]
rs72974866	0.88[ASN][1000 genomes]
rs72974869	0.83[ASN][1000 genomes]
rs72976852	1.00[ASN][1000 genomes]
rs72989228	0.81[ASN][1000 genomes]
rs7929705	0.81[ASN][1000 genomes]
rs7939193	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[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
rs2140892	PAAF1	cis	lymphoblastoid	seeQTL
rs2140892	KRTAP5-11	cis	cerebellum	SCAN
rs2140892	GDPD4	cis	parietal	SCAN
rs2140892	FLJ11848	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73374400-73427200	Weak transcription	A549	lung
2	chr11:73382200-73436000	Weak transcription	Small Intestine	intestine
3	chr11:73382200-73441200	Weak transcription	Stomach Mucosa	stomach
4	chr11:73383400-73427200	Weak transcription	Fetal Heart	heart
5	chr11:73384000-73427600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:73389000-73445400	Weak transcription	Fetal Brain Male	brain
8	chr11:73389200-73427400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:73389200-73440200	Weak transcription	Right Ventricle	heart
10	chr11:73390800-73429600	Weak transcription	NHLF	lung
11	chr11:73391000-73433600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:73394400-73430200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:73396000-73448000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:73397800-73426600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:73400400-73449400	Weak transcription	Psoas Muscle	Psoas
16	chr11:73404400-73424200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:73404400-73427400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:73405200-73429600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:73405400-73426400	Weak transcription	Brain Substantia Nigra	brain
20	chr11:73407000-73432000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:73409600-73447800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:73410000-73423000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr11:73410000-73434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:73410200-73427400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:73410600-73423400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:73410800-73431800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:73411000-73426400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:73411000-73447600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:73411000-73460000	Weak transcription	Colonic Mucosa	Colon
30	chr11:73412400-73423000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:73413400-73440400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:73413400-73470800	Weak transcription	Esophagus	oesophagus
33	chr11:73413600-73447600	Weak transcription	Left Ventricle	heart
34	chr11:73415000-73425400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:73415000-73436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:73415000-73470200	Weak transcription	Aorta	Aorta
37	chr11:73416000-73423000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:73416400-73429600	Weak transcription	Ovary	ovary
39	chr11:73417000-73440400	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:73417200-73426400	Weak transcription	Brain Angular Gyrus	brain
41	chr11:73417200-73427200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:73417200-73469600	Weak transcription	Fetal Kidney	kidney
43	chr11:73417800-73427800	Weak transcription	Fetal Lung	lung
44	chr11:73417800-73429600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:73418200-73423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:73418200-73443400	Weak transcription	Brain Germinal Matrix	brain
47	chr11:73418400-73463200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr11:73418600-73429600	Weak transcription	HSMMtube	muscle
49	chr11:73419000-73423000	Weak transcription	HUVEC	blood vessel
50	chr11:73419000-73425600	Weak transcription	GM12878-XiMat	blood

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