Variant report

Variant	rs12786236
Chromosome Location	chr11:9738606-9738607
allele	A/C
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	ELF1	chr11:9738236-9738659	K562	blood:	n/a	chr11:9738437-9738450
2	IRF4	chr11:9738144-9738713	GM12878	blood:	n/a	n/a
3	ATF2	chr11:9737913-9738893	GM12878	blood:	n/a	n/a
4	EBF1	chr11:9738281-9738687	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:9738114-9738807	GM12892	blood:	n/a	n/a
6	FOS	chr11:9738349-9738683	MCF10A-Er-Src	breast:	n/a	chr11:9738506-9738517
7	JUN	chr11:9738285-9738915	HUVEC	blood vessel:	n/a	chr11:9738699-9738712 chr11:9738730-9738739
8	REST	chr11:9738277-9738620	Hela-S3	cervix:	n/a	n/a
9	FOXM1	chr11:9737657-9738804	GM12878	blood:	n/a	n/a
10	STAT5A	chr11:9737943-9738845	GM12878	blood:	n/a	n/a
11	FOXM1	chr11:9737959-9738833	GM12878	blood:	n/a	n/a
12	FOS	chr11:9738240-9738798	HUVEC	blood vessel:	n/a	chr11:9738730-9738739 chr11:9738506-9738517
13	MAFF	chr11:9738279-9738696	K562	blood:	n/a	n/a
14	SPI1	chr11:9738175-9738716	HL-60	blood:	n/a	n/a
15	FOS	chr11:9738339-9738689	MCF10A-Er-Src	breast:	n/a	chr11:9738506-9738517
16	POLR2A	chr11:9738204-9738691	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr11:9738041-9738766	HL-60	blood:	n/a	n/a
18	BACH1	chr11:9738334-9738691	K562	blood:	n/a	n/a
19	POLR2A	chr11:9737957-9738810	GM12892	blood:	n/a	n/a
20	MYC	chr11:9738332-9738616	K562	blood:	n/a	n/a
21	JUND	chr11:9738558-9738730	HepG2	liver:	n/a	n/a
22	TEAD4	chr11:9738105-9738739	K562	blood:	n/a	n/a
23	JUND	chr11:9738326-9738700	K562	blood:	n/a	n/a
24	POLR2A	chr11:9738398-9738625	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr11:9738063-9738783	GM12892	blood:	n/a	n/a
26	CBX3	chr11:9738138-9738644	K562	blood:	n/a	n/a
27	RUNX3	chr11:9737766-9738823	GM12878	blood:	n/a	n/a
28	EP300	chr11:9737957-9738789	GM12878	blood:	n/a	chr11:9738728-9738737 chr11:9738727-9738741 chr11:9738704-9738712
29	MTA3	chr11:9737247-9738898	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:9737228-9738850	GM12892	blood:	n/a	n/a
31	RELA	chr11:9737416-9738706	GM10847	blood:	n/a	n/a
32	E2F4	chr11:9738597-9738669	MCF10A-Er-Src	breast:	n/a	n/a
33	MTA3	chr11:9738182-9738745	GM12878	blood:	n/a	n/a
34	STAT3	chr11:9738433-9738736	MCF10A-Er-Src	breast:	n/a	n/a
35	JUN	chr11:9738589-9738754	HepG2	liver:	n/a	chr11:9738699-9738712 chr11:9738730-9738739
36	EBF1	chr11:9738236-9738722	GM12878	blood:	n/a	n/a
37	EP300	chr11:9738317-9738700	GM12878	blood:	n/a	n/a
38	SPI1	chr11:9738103-9738724	GM12891	blood:	n/a	n/a
39	MAFK	chr11:9738315-9738703	K562	blood:	n/a	n/a
40	MYC	chr11:9738440-9738645	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr11:9738334-9738759	MCF10A-Er-Src	breast:	n/a	chr11:9738730-9738739 chr11:9738506-9738517
42	STAT3	chr11:9738375-9738772	MCF10A-Er-Src	breast:	n/a	n/a
43	RELA	chr11:9737345-9738704	GM12891	blood:	n/a	n/a
44	RUNX3	chr11:9737949-9738746	GM12878	blood:	n/a	n/a
45	CREB1	chr11:9738248-9738786	GM12878	blood:	n/a	n/a
46	TBL1XR1	chr11:9738386-9738652	K562	blood:	n/a	n/a
47	GATA2	chr11:9738203-9738636	HUVEC	blood vessel:	n/a	n/a
48	WRNIP1	chr11:9738089-9738680	GM12878	blood:	n/a	n/a
49	CREB1	chr11:9738142-9738888	GM12878	blood:	n/a	n/a
50	EBF1	chr11:9738271-9738722	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SWAP70	TF binding region

Extended variants
information (count: 166 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10770056	0.86[EUR][1000 genomes]
rs10770057	0.82[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	0.86[EUR][1000 genomes]
rs10840291	0.86[EUR][1000 genomes]
rs10840292	0.86[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	0.86[EUR][1000 genomes]
rs11042481	0.88[EUR][1000 genomes]
rs11042482	0.88[EUR][1000 genomes]
rs11042483	0.88[EUR][1000 genomes]
rs11042486	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.84[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]
rs11604967	0.81[AMR][1000 genomes]
rs11607321	1.00[ASN][1000 genomes]
rs11607582	1.00[CHB][hapmap]
rs11607900	1.00[ASN][1000 genomes]
rs12271923	0.86[EUR][1000 genomes]
rs12272107	0.86[EUR][1000 genomes]
rs12272277	0.86[EUR][1000 genomes]
rs12280169	0.87[EUR][1000 genomes]
rs12280320	0.86[EUR][1000 genomes]
rs12283521	0.85[EUR][1000 genomes]
rs12291809	0.81[EUR][1000 genomes]
rs12362879	1.00[ASN][1000 genomes]
rs12364089	1.00[ASN][1000 genomes]
rs12419564	1.00[CHB][hapmap]
rs12421878	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]
rs12574474	1.00[YRI][hapmap]
rs12574508	1.00[YRI][hapmap]
rs12574765	1.00[YRI][hapmap]
rs12576763	1.00[YRI][hapmap]
rs12577960	1.00[YRI][hapmap]
rs12578023	1.00[YRI][hapmap]
rs12789209	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789429	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794270	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797744	1.00[ASN][1000 genomes]
rs12801958	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12803440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805683	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807017	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs12808226	1.00[CHB][hapmap]
rs1390679	0.88[EUR][1000 genomes]
rs1390681	0.88[EUR][1000 genomes]
rs1390682	0.88[EUR][1000 genomes]
rs1390683	0.88[EUR][1000 genomes]
rs1390684	0.88[EUR][1000 genomes]
rs1435462	0.88[EUR][1000 genomes]
rs1695613	0.96[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs17268632	1.00[CHB][hapmap]
rs17270804	1.00[CHB][hapmap]
rs17355675	1.00[CHB][hapmap]
rs17355924	1.00[CHB][hapmap]
rs1874476	0.88[EUR][1000 genomes]
rs1960386	0.87[EUR][1000 genomes]
rs1960387	0.88[EUR][1000 genomes]
rs2117698	0.86[EUR][1000 genomes]
rs2117699	0.83[EUR][1000 genomes]
rs2132565	0.88[EUR][1000 genomes]
rs2132566	0.88[EUR][1000 genomes]
rs2132567	0.88[EUR][1000 genomes]
rs2164311	0.87[EUR][1000 genomes]
rs2252354	0.87[EUR][1000 genomes]
rs2336805	0.88[EUR][1000 genomes]
rs2453831	0.96[CEU][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2453832	0.81[EUR][1000 genomes]
rs2454611	0.81[EUR][1000 genomes]
rs2454612	0.81[EUR][1000 genomes]
rs2572934	0.88[EUR][1000 genomes]
rs2572935	0.87[EUR][1000 genomes]
rs2572943	0.88[EUR][1000 genomes]
rs2572944	0.87[EUR][1000 genomes]
rs2572945	0.83[EUR][1000 genomes]
rs2645007	0.81[EUR][1000 genomes]
rs2645008	0.80[EUR][1000 genomes]
rs2645010	0.81[EUR][1000 genomes]
rs2645011	0.81[EUR][1000 genomes]
rs2645025	0.88[EUR][1000 genomes]
rs2649046	0.88[EUR][1000 genomes]
rs2649048	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs34063054	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35806232	1.00[ASN][1000 genomes]
rs36089180	1.00[ASN][1000 genomes]
rs368731	0.87[EUR][1000 genomes]
rs369737	0.84[CEU][hapmap]
rs385846	0.81[EUR][1000 genomes]
rs389534	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs392815	0.87[EUR][1000 genomes]
rs397250	1.00[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs397602	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs397686	0.96[CEU][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs399898	0.87[EUR][1000 genomes]
rs408569	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs414109	0.87[EUR][1000 genomes]
rs416804	0.88[EUR][1000 genomes]
rs418931	0.88[EUR][1000 genomes]
rs419412	0.87[EUR][1000 genomes]
rs422061	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs424455	0.84[EUR][1000 genomes]
rs428747	0.87[EUR][1000 genomes]
rs429546	0.87[EUR][1000 genomes]
rs431908	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs435079	0.84[EUR][1000 genomes]
rs440523	0.88[EUR][1000 genomes]
rs441965	0.85[EUR][1000 genomes]
rs442722	0.87[EUR][1000 genomes]
rs443576	0.86[EUR][1000 genomes]
rs446146	0.88[EUR][1000 genomes]
rs447601	0.88[EUR][1000 genomes]
rs4478983	0.87[EUR][1000 genomes]
rs449005	0.88[EUR][1000 genomes]
rs452169	0.81[EUR][1000 genomes]
rs476163	0.84[EUR][1000 genomes]
rs4910060	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910075	1.00[CHB][hapmap]
rs4910486	1.00[ASN][1000 genomes]
rs4910487	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs4910488	1.00[ASN][1000 genomes]
rs4910491	0.88[EUR][1000 genomes]
rs4910492	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910493	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910494	0.87[EUR][1000 genomes]
rs4910495	0.87[EUR][1000 genomes]
rs4910496	0.86[EUR][1000 genomes]
rs4910497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910505	1.00[CHB][hapmap]
rs4993191	0.83[EUR][1000 genomes]
rs534901	0.88[EUR][1000 genomes]
rs56043731	1.00[ASN][1000 genomes]
rs581004	0.84[EUR][1000 genomes]
rs58960327	0.81[EUR][1000 genomes]
rs60466677	0.88[EUR][1000 genomes]
rs61878110	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67867011	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108907	1.00[YRI][hapmap]
rs7116226	0.91[EUR][1000 genomes]
rs7117197	0.80[EUR][1000 genomes]
rs72852112	1.00[ASN][1000 genomes]
rs7935643	0.88[EUR][1000 genomes]
rs7938818	0.88[EUR][1000 genomes]
rs7943610	1.00[CHB][hapmap]
rs7949818	0.88[EUR][1000 genomes]
rs892851	0.83[EUR][1000 genomes]
rs892852	0.83[EUR][1000 genomes]
rs892856	0.83[EUR][1000 genomes]
rs920080	0.88[EUR][1000 genomes]
rs920082	1.00[CEU][hapmap];0.83[TSI][hapmap];0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12786236	ZNF214	cis	cerebellum	SCAN
rs12786236	SWAP70	cis	cerebellum	SCAN
rs12786236	TRIM22	cis	cerebellum	SCAN
rs12786236	PRRT3	trans	cerebellum	SCAN
rs12786236	ASCL3	cis	parietal	SCAN

Chromatin state (count:107 , 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	chr11:9717600-9738800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:9717600-9739200	Weak transcription	NHLF	lung
5	chr11:9717600-9751000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:9717600-9751000	Weak transcription	Ovary	ovary
7	chr11:9718200-9749600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:9724000-9739400	Weak transcription	Fetal Lung	lung
9	chr11:9725200-9740800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:9725200-9749600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr11:9725400-9741800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:9725600-9748000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:9726600-9749600	Weak transcription	Liver	Liver
14	chr11:9729600-9755400	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr11:9730400-9739400	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:9730600-9739400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:9730600-9739400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:9730600-9739400	Weak transcription	Small Intestine	intestine
19	chr11:9730600-9747200	Weak transcription	Pancreas	Pancrea
20	chr11:9730600-9758200	Weak transcription	Esophagus	oesophagus
21	chr11:9731200-9740800	Weak transcription	Brain Substantia Nigra	brain
22	chr11:9732000-9754000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:9733200-9738800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:9733200-9743800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:9733200-9754000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:9733400-9739000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:9733400-9739400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:9733400-9749400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:9733400-9754200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:9733600-9739400	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:9733600-9739400	Weak transcription	Fetal Kidney	kidney
32	chr11:9733600-9741600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:9733600-9757000	Weak transcription	Fetal Brain Female	brain
34	chr11:9733600-9761600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:9733800-9739600	Weak transcription	Brain Angular Gyrus	brain
36	chr11:9733800-9743800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr11:9733800-9759800	Weak transcription	Fetal Heart	heart
38	chr11:9735000-9739400	Weak transcription	Stomach Mucosa	stomach
39	chr11:9736400-9739400	Weak transcription	HepG2	liver
40	chr11:9736400-9741200	Weak transcription	Primary T cells from cord blood	blood
41	chr11:9737200-9739600	Enhancers	Spleen	Spleen
42	chr11:9737400-9738800	Flanking Active TSS	GM12878-XiMat	blood
43	chr11:9737400-9739400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:9737400-9740000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:9737400-9740000	Genic enhancers	NHDF-Ad	bronchial
46	chr11:9737600-9739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:9737600-9739000	Weak transcription	Fetal Intestine Large	intestine
48	chr11:9737600-9739000	Weak transcription	Fetal Intestine Small	intestine
49	chr11:9737600-9739800	Enhancers	Adipose Nuclei	Adipose
50	chr11:9737600-9740000	Genic enhancers	Primary B cells from cord blood	blood

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