Variant report

Variant	rs12421878
Chromosome Location	chr11:9737838-9737839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr11:9737837-9738068	GM12878	blood:	n/a	n/a
2	FOXM1	chr11:9737657-9738804	GM12878	blood:	n/a	n/a
3	RUNX3	chr11:9737766-9738823	GM12878	blood:	n/a	n/a
4	MTA3	chr11:9737247-9738898	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:9737228-9738850	GM12892	blood:	n/a	n/a
6	RELA	chr11:9737416-9738706	GM10847	blood:	n/a	n/a
7	RELA	chr11:9737345-9738704	GM12891	blood:	n/a	n/a
8	BCLAF1	chr11:9737807-9738818	GM12878	blood:	n/a	chr11:9738732-9738741
9	NFIC	chr11:9737792-9738901	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:9737727-9738955	HUVEC	blood vessel:	n/a	n/a
11	RELA	chr11:9737412-9738687	GM19099	blood:	n/a	n/a
12	CEBPB	chr11:9737798-9738724	GM12878	blood:	n/a	n/a
13	SPI1	chr11:9737736-9739030	GM12878	blood:	n/a	chr11:9738732-9738741
14	NFIC	chr11:9737676-9738870	GM12878	blood:	n/a	n/a
15	RELA	chr11:9737452-9738719	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9601830..9604775-chr11:9735328..9738151,2	K562	blood:

Variant related genes	Relation type
SWAP70	TF binding region
ENSG00000166483	Chromatin interaction
ENSG00000243869	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10770056	0.89[EUR][1000 genomes]
rs10840283	1.00[ASN][1000 genomes]
rs10840284	1.00[ASN][1000 genomes]
rs10840286	1.00[ASN][1000 genomes]
rs10840287	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10840290	0.84[EUR][1000 genomes]
rs10840291	0.83[EUR][1000 genomes]
rs10840292	0.83[EUR][1000 genomes]
rs10840315	1.00[CHB][hapmap]
rs10840325	1.00[CHB][hapmap]
rs11042457	1.00[ASN][1000 genomes]
rs11042462	1.00[ASN][1000 genomes]
rs11042464	1.00[ASN][1000 genomes]
rs11042466	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11042467	1.00[ASN][1000 genomes]
rs11042476	0.83[EUR][1000 genomes]
rs11042481	0.85[EUR][1000 genomes]
rs11042482	0.85[EUR][1000 genomes]
rs11042483	0.85[EUR][1000 genomes]
rs11042486	1.00[CHB][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042500	1.00[CHB][hapmap]
rs11042511	1.00[CHB][hapmap]
rs11042526	1.00[CHB][hapmap]
rs11600183	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11601008	1.00[ASN][1000 genomes]
rs11603527	1.00[ASN][1000 genomes]
rs11607321	1.00[ASN][1000 genomes]
rs11607582	1.00[CHB][hapmap]
rs11607900	1.00[ASN][1000 genomes]
rs12271923	0.83[EUR][1000 genomes]
rs12272107	0.83[EUR][1000 genomes]
rs12272277	0.83[EUR][1000 genomes]
rs12280169	0.84[EUR][1000 genomes]
rs12280320	0.83[EUR][1000 genomes]
rs12283521	0.81[EUR][1000 genomes]
rs12362879	1.00[ASN][1000 genomes]
rs12364089	1.00[ASN][1000 genomes]
rs12419564	1.00[CHB][hapmap]
rs12786236	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789209	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789429	1.00[ASN][1000 genomes]
rs12794270	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797744	1.00[ASN][1000 genomes]
rs12801958	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12803440	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805683	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807017	1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12808226	1.00[CHB][hapmap]
rs1390679	0.85[EUR][1000 genomes]
rs1390681	0.85[EUR][1000 genomes]
rs1390682	0.85[EUR][1000 genomes]
rs1390683	0.85[EUR][1000 genomes]
rs1390684	0.85[EUR][1000 genomes]
rs1435462	0.85[EUR][1000 genomes]
rs1695613	0.96[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs17268632	1.00[CHB][hapmap]
rs17270804	1.00[CHB][hapmap]
rs17355675	1.00[CHB][hapmap]
rs17355924	1.00[CHB][hapmap]
rs1874476	0.85[EUR][1000 genomes]
rs1960386	0.84[EUR][1000 genomes]
rs1960387	0.85[EUR][1000 genomes]
rs2117698	0.90[EUR][1000 genomes]
rs2117699	0.86[EUR][1000 genomes]
rs2132565	0.85[EUR][1000 genomes]
rs2132566	0.85[EUR][1000 genomes]
rs2132567	0.85[EUR][1000 genomes]
rs2164311	0.91[EUR][1000 genomes]
rs2252354	0.84[EUR][1000 genomes]
rs2336805	0.85[EUR][1000 genomes]
rs2453831	0.96[CEU][hapmap]
rs2572934	0.85[EUR][1000 genomes]
rs2572935	0.84[EUR][1000 genomes]
rs2572943	0.85[EUR][1000 genomes]
rs2572944	0.84[EUR][1000 genomes]
rs2645012	0.80[EUR][1000 genomes]
rs2645025	0.85[EUR][1000 genomes]
rs2649046	0.85[EUR][1000 genomes]
rs2649048	1.00[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs34063054	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35806232	1.00[ASN][1000 genomes]
rs360047	0.83[EUR][1000 genomes]
rs360049	0.81[EUR][1000 genomes]
rs36089180	1.00[ASN][1000 genomes]
rs368731	0.84[EUR][1000 genomes]
rs369737	0.84[CEU][hapmap]
rs389534	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs392815	0.84[EUR][1000 genomes]
rs397250	1.00[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs397602	1.00[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs397686	0.96[CEU][hapmap]
rs399898	0.84[EUR][1000 genomes]
rs408569	1.00[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs414109	0.84[EUR][1000 genomes]
rs416804	0.85[EUR][1000 genomes]
rs418931	0.85[EUR][1000 genomes]
rs419412	0.84[EUR][1000 genomes]
rs422061	1.00[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs424455	0.87[EUR][1000 genomes]
rs428747	0.84[EUR][1000 genomes]
rs429546	0.84[EUR][1000 genomes]
rs431908	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs435079	0.88[EUR][1000 genomes]
rs440523	0.85[EUR][1000 genomes]
rs441965	0.82[EUR][1000 genomes]
rs442722	0.84[EUR][1000 genomes]
rs443576	0.83[EUR][1000 genomes]
rs446146	0.85[EUR][1000 genomes]
rs447601	0.85[EUR][1000 genomes]
rs4478983	0.84[EUR][1000 genomes]
rs449005	0.85[EUR][1000 genomes]
rs476163	0.88[EUR][1000 genomes]
rs4910060	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910075	1.00[CHB][hapmap]
rs4910486	1.00[ASN][1000 genomes]
rs4910487	1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs4910488	1.00[ASN][1000 genomes]
rs4910491	0.85[EUR][1000 genomes]
rs4910492	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910493	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910494	0.85[EUR][1000 genomes]
rs4910495	0.85[EUR][1000 genomes]
rs4910496	0.84[EUR][1000 genomes]
rs4910497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910505	1.00[CHB][hapmap]
rs4993191	0.87[EUR][1000 genomes]
rs534901	0.85[EUR][1000 genomes]
rs56043731	1.00[ASN][1000 genomes]
rs581004	0.87[EUR][1000 genomes]
rs60466677	0.85[EUR][1000 genomes]
rs61878110	0.90[EUR][1000 genomes]
rs67867011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116226	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7117197	0.82[EUR][1000 genomes]
rs72852112	1.00[ASN][1000 genomes]
rs7935643	0.85[EUR][1000 genomes]
rs7938818	0.85[EUR][1000 genomes]
rs7943610	1.00[CHB][hapmap]
rs7949818	0.85[EUR][1000 genomes]
rs892851	0.87[EUR][1000 genomes]
rs892852	0.87[EUR][1000 genomes]
rs892856	0.87[EUR][1000 genomes]
rs920080	0.85[EUR][1000 genomes]
rs920082	1.00[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12421878	OVCH2	cis	parietal	SCAN
rs12421878	ASCL3	cis	parietal	SCAN
rs12421878	RIC3	cis	cerebellum	SCAN
rs12421878	OR2D2	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9710200-9758400	Weak transcription	Psoas Muscle	Psoas
2	chr11:9711400-9754400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:9716000-9738000	Weak transcription	HMEC	breast
4	chr11:9717600-9738800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:9717600-9739200	Weak transcription	NHLF	lung
6	chr11:9717600-9751000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:9717600-9751000	Weak transcription	Ovary	ovary
8	chr11:9718200-9749600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:9724000-9739400	Weak transcription	Fetal Lung	lung
10	chr11:9725200-9738200	Weak transcription	Fetal Thymus	thymus
11	chr11:9725200-9740800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:9725200-9749600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr11:9725400-9741800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:9725600-9748000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:9726600-9749600	Weak transcription	Liver	Liver
16	chr11:9729600-9755400	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr11:9730400-9739400	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:9730600-9738000	Weak transcription	NH-A	brain
19	chr11:9730600-9738200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:9730600-9739400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:9730600-9739400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:9730600-9739400	Weak transcription	Small Intestine	intestine
23	chr11:9730600-9747200	Weak transcription	Pancreas	Pancrea
24	chr11:9730600-9758200	Weak transcription	Esophagus	oesophagus
25	chr11:9730800-9738000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:9730800-9738200	Weak transcription	Lung	lung
27	chr11:9730800-9738200	Weak transcription	HSMMtube	muscle
28	chr11:9731200-9740800	Weak transcription	Brain Substantia Nigra	brain
29	chr11:9732000-9754000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:9733200-9738800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:9733200-9743800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:9733200-9754000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:9733400-9739000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:9733400-9739400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:9733400-9749400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:9733400-9754200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr11:9733600-9738000	Weak transcription	Aorta	Aorta
38	chr11:9733600-9738200	Weak transcription	Right Atrium	heart
39	chr11:9733600-9739400	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:9733600-9739400	Weak transcription	Fetal Kidney	kidney
41	chr11:9733600-9741600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:9733600-9757000	Weak transcription	Fetal Brain Female	brain
43	chr11:9733600-9761600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:9733800-9739600	Weak transcription	Brain Angular Gyrus	brain
45	chr11:9733800-9743800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:9733800-9759800	Weak transcription	Fetal Heart	heart
47	chr11:9734600-9738200	Strong transcription	HSMM	muscle
48	chr11:9734800-9738200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:9735000-9738200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:9735000-9738400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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