Variant report

Variant	rs3930513
Chromosome Location	chr11:32455527-32455528
allele	G/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	CTCF	chr11:32455500-32455650	GM12871	blood:	n/a	n/a
2	POLR2A	chr11:32455166-32455662	K562	blood:	n/a	n/a
3	CBX3	chr11:32455237-32455642	K562	blood:	n/a	n/a
4	SUZ12	chr11:32453725-32461544	NT2-D1	testis:	n/a	n/a
5	BACH1	chr11:32455379-32455942	K562	blood:	n/a	n/a
6	JUN	chr11:32453532-32456818	K562	blood:	n/a	chr11:32453717-32453725
7	CTBP2	chr11:32454448-32456818	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:32455132-32457736	K562	blood:	n/a	n/a
9	POLR2A	chr11:32453940-32456452	K562	blood:	n/a	n/a
10	MAX	chr11:32454537-32457687	K562	blood:	n/a	chr11:32457467-32457477
11	MAX	chr11:32455170-32457723	K562	blood:	n/a	chr11:32457467-32457477
12	EP300	chr11:32455142-32455787	K562	blood:	n/a	n/a
13	CCNT2	chr11:32455203-32455550	K562	blood:	n/a	n/a
14	TAL1	chr11:32455399-32456659	K562	blood:	n/a	n/a
15	MYC	chr11:32455256-32457710	NB4	blood:	n/a	chr11:32457467-32457477
16	RCOR1	chr11:32454151-32456441	K562	blood:	n/a	n/a
17	TEAD4	chr11:32454979-32456457	K562	blood:	n/a	n/a
18	IRF1	chr11:32455262-32456419	K562	blood:	n/a	chr11:32455294-32455308
19	HEY1	chr11:32455201-32455531	K562	blood:	n/a	n/a
20	MAFK	chr11:32454972-32455723	K562	blood:	n/a	chr11:32455344-32455360 chr11:32455345-32455359
21	MAX	chr11:32455156-32455690	K562	blood:	n/a	n/a
22	RCOR1	chr11:32455243-32455896	K562	blood:	n/a	n/a
23	MAX	chr11:32454143-32458628	NB4	blood:	n/a	chr11:32457467-32457477
24	MYC	chr11:32455104-32457646	K562	blood:	n/a	chr11:32457467-32457477
25	JUND	chr11:32454141-32456484	K562	blood:	n/a	n/a
26	POLR2A	chr11:32453980-32457577	K562	blood:	n/a	n/a
27	REST	chr11:32455487-32456475	HL-60	blood:	n/a	chr11:32455640-32455647 chr11:32455796-32455816
28	TAF1	chr11:32454924-32455560	K562	blood:	n/a	n/a
29	ZMIZ1	chr11:32455324-32456379	K562	blood:	n/a	n/a
30	POLR2A	chr11:32455061-32456487	K562	blood:	n/a	n/a
31	SUZ12	chr11:32453771-32458890	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr11:32454161-32457678	K562	blood:	n/a	n/a
33	POLR2A	chr11:32455366-32457646	HL-60	blood:	n/a	n/a
34	CUX1	chr11:32455110-32455584	K562	blood:	n/a	n/a
35	HCFC1	chr11:32455153-32455603	K562	blood:	n/a	n/a
36	HEY1	chr11:32455141-32456962	K562	blood:	n/a	chr11:32456092-32456107 chr11:32456933-32456948 chr11:32456201-32456216
37	TBP	chr11:32453973-32457616	K562	blood:	n/a	n/a
38	BHLHE40	chr11:32455078-32456429	K562	blood:	n/a	n/a
39	POLR2A	chr11:32454208-32457616	K562	blood:	n/a	n/a
40	HMGN3	chr11:32454773-32457488	K562	blood:	n/a	n/a
41	POLR2A	chr11:32453512-32457942	NB4	blood:	n/a	n/a
42	SPI1	chr11:32455461-32456536	HL-60	blood:	n/a	n/a
43	MAFF	chr11:32455226-32455669	K562	blood:	n/a	chr11:32455345-32455359
44	CHD2	chr11:32454955-32455615	K562	blood:	n/a	n/a
45	MYC	chr11:32454126-32457534	K562	blood:	n/a	chr11:32457467-32457477
46	TBL1XR1	chr11:32454629-32455675	K562	blood:	n/a	n/a
47	POLR2A	chr11:32453842-32457744	K562	blood:	n/a	n/a
48	POLR2A	chr11:32454637-32457626	K562	blood:	n/a	n/a
49	TRIM28	chr11:32455482-32456461	K562	blood:	n/a	n/a
50	SIN3AK20	chr11:32455057-32456473	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:32455369..32457971-chr11:32914210..32916339,2	K562	blood:
2	chr11:32455462..32457058-chr11:32608687..32611459,2	K562	blood:
3	chr11:32455134..32460391-chr11:32603988..32611641,10	K562	blood:
4	chr11:32455134..32458517-chr11:32603988..32607695,5	K562	blood:
5	chr11:32453512..32456485-chr11:32618384..32621260,2	K562	blood:

Variant related genes	Relation type
WT1-AS	TF binding region
WT1	TF binding region
ENSG00000060749	Chromatin interaction
ENSG00000149100	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10742277	0.91[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835917	0.82[CHD][hapmap];0.80[TSI][hapmap]
rs11031783	0.90[ASN][1000 genomes]
rs11031784	0.90[ASN][1000 genomes]
rs11031796	0.80[AMR][1000 genomes]
rs2234580	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234585	0.83[ASN][1000 genomes]
rs2301250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301251	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301252	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301253	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301254	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809062	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3858445	0.82[CHD][hapmap]
rs3858446	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3858447	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3858448	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3858449	0.81[CHD][hapmap]
rs3858454	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs3886325	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140413	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4275604	0.87[AFR][1000 genomes]
rs5030141	0.81[CHD][hapmap]
rs5030171	0.83[ASN][1000 genomes]
rs5030176	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5030178	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5030179	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103000	0.86[AFR][1000 genomes]
rs7110547	0.92[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7120686	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7126322	0.80[AMR][1000 genomes]
rs7946086	0.81[CEU][hapmap];0.86[GIH][hapmap]

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	nsv832108	chr11:32395937-32560583	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1044547	chr11:32435753-32465233	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2753303	chr11:32447324-32494924	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1051559	chr11:32447347-32465233	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3930513	WT1AS	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32450200-32457400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr11:32453400-32459600	Active TSS	Right Atrium	heart
3	chr11:32454400-32455600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
4	chr11:32454400-32456200	Bivalent Enhancer	Liver	Liver
5	chr11:32454400-32456200	Bivalent/Poised TSS	Fetal Kidney	kidney
6	chr11:32454400-32456400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr11:32454600-32455800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:32454600-32455800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:32454600-32455800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
10	chr11:32454600-32456400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:32454600-32456400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:32454600-32456600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr11:32454600-32456600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
14	chr11:32454600-32456800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
15	chr11:32454600-32457000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:32454600-32458600	Bivalent/Poised TSS	Left Ventricle	heart
17	chr11:32454600-32458800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
18	chr11:32454600-32459800	Active TSS	Ovary	ovary
19	chr11:32454800-32455600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:32454800-32455600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
21	chr11:32454800-32455600	Bivalent Enhancer	Fetal Thymus	thymus
22	chr11:32454800-32455600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
23	chr11:32454800-32456000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
24	chr11:32454800-32456000	Enhancers	Gastric	stomach
25	chr11:32454800-32456000	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr11:32454800-32456200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr11:32454800-32456200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:32454800-32456200	Bivalent/Poised TSS	Colonic Mucosa	Colon
29	chr11:32454800-32456200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr11:32454800-32456400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:32454800-32456400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
32	chr11:32454800-32456400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
33	chr11:32454800-32456600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:32454800-32456600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr11:32454800-32457800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:32454800-32457800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:32454800-32458200	Bivalent Enhancer	Esophagus	oesophagus
38	chr11:32454800-32458600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
39	chr11:32455000-32455600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:32455000-32455600	Bivalent Enhancer	Thymus	Thymus
41	chr11:32455000-32456000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr11:32455000-32457400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr11:32455000-32459400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
44	chr11:32455200-32455600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
45	chr11:32455200-32455600	Bivalent Enhancer	Primary T cells from cord blood	blood
46	chr11:32455200-32455600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:32455200-32455600	Bivalent Enhancer	Brain Anterior Caudate	brain
48	chr11:32455200-32455600	Bivalent Enhancer	NHDF-Ad	bronchial
49	chr11:32455200-32456000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:32455200-32456000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

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