Variant report

Variant	rs3858445
Chromosome Location	chr11:32442636-32442637
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	MYC	chr11:32442634-32442708	K562	blood:	n/a	n/a
2	GATA3	chr11:32442273-32443070	T-47D	breast:	n/a	chr11:32442878-32442888 chr11:32442877-32442889 chr11:32442892-32442900
3	EBF1	chr11:32442289-32443064	GM12878	blood:	n/a	n/a
4	ZMIZ1	chr11:32442369-32443007	K562	blood:	n/a	n/a
5	RELA	chr11:32442305-32443062	GM19099	blood:	n/a	n/a
6	TCF12	chr11:32442183-32442788	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr11:32442252-32445401	K562	blood:	n/a	n/a
8	YY1	chr11:32442463-32442799	K562	blood:	n/a	n/a
9	MAX	chr11:32442464-32442948	K562	blood:	n/a	n/a
10	RELA	chr11:32442315-32443024	GM18951	blood:	n/a	n/a
11	ATF1	chr11:32442306-32443006	K562	blood:	n/a	n/a
12	CCNT2	chr11:32442431-32442884	K562	blood:	n/a	n/a
13	RELA	chr11:32442262-32443009	GM12891	blood:	n/a	n/a
14	ELK1	chr11:32442615-32442741	GM12878	blood:	n/a	n/a
15	GATA3	chr11:32442175-32443165	SK-N-SH	brain:	n/a	chr11:32442878-32442888 chr11:32442877-32442889 chr11:32442892-32442900
16	ETS1	chr11:32442347-32442673	GM12878	blood:	n/a	chr11:32442549-32442563 chr11:32442551-32442562 chr11:32442551-32442564
17	MAX	chr11:32442317-32443799	NB4	blood:	n/a	n/a
18	RFX5	chr11:32442217-32442702	K562	blood:	n/a	n/a
19	YY1	chr11:32442536-32442785	GM12878	blood:	n/a	n/a
20	TCF7L2	chr11:32442491-32442956	PANC-1	pancreas:	n/a	n/a
21	NFIC	chr11:32442297-32442680	GM12878	blood:	n/a	chr11:32442364-32442381 chr11:32442365-32442381
22	ARID3A	chr11:32442369-32442946	K562	blood:	n/a	n/a
23	MTA3	chr11:32442294-32442974	GM12878	blood:	n/a	n/a
24	CEBPB	chr11:32442484-32443041	K562	blood:	n/a	n/a
25	NFIC	chr11:32442301-32442824	SK-N-SH	brain:	n/a	chr11:32442364-32442381 chr11:32442365-32442381
26	GATA3	chr11:32442262-32443415	T-47D	breast:	n/a	chr11:32442878-32442888 chr11:32443279-32443300 chr11:32442877-32442889 chr11:32442892-32442900
27	WRNIP1	chr11:32442410-32442910	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:32442317-32443009	K562	blood:	n/a	n/a
29	REST	chr11:32442258-32443016	PFSK-1	brain:	n/a	n/a
30	TCF12	chr11:32442250-32443158	SK-N-SH	brain:	n/a	n/a
31	CEBPD	chr11:32442308-32443149	K562	blood:	n/a	n/a
32	UBTF	chr11:32442435-32442800	K562	blood:	n/a	n/a
33	TAL1	chr11:32442468-32443071	K562	blood:	n/a	chr11:32442869-32442887
34	MYC	chr11:32442368-32443459	K562	blood:	n/a	n/a
35	RCOR1	chr11:32442292-32443717	K562	blood:	n/a	n/a
36	RUNX3	chr11:32442279-32443102	GM12878	blood:	n/a	n/a
37	EP300	chr11:32442304-32443496	K562	blood:	n/a	chr11:32443261-32443275 chr11:32443179-32443188 chr11:32443383-32443390 chr11:32443144-32443153
38	CHD2	chr11:32442262-32442724	K562	blood:	n/a	n/a
39	TAF1	chr11:32442312-32442948	PFSK-1	brain:	n/a	n/a
40	NR2F2	chr11:32442247-32443430	K562	blood:	n/a	n/a
41	GATA1	chr11:32441707-32443572	PBDE	blood:	n/a	chr11:32442878-32442888 chr11:32443279-32443300 chr11:32442877-32442889 chr11:32442892-32442900
42	GTF2B	chr11:32442532-32442741	K562	blood:	n/a	n/a
43	HCFC1	chr11:32442365-32443015	K562	blood:	n/a	n/a
44	MAFF	chr11:32442410-32442876	K562	blood:	n/a	n/a
45	TBL1XR1	chr11:32442417-32442942	K562	blood:	n/a	n/a
46	JUND	chr11:32442272-32443013	K562	blood:	n/a	n/a
47	EP300	chr11:32442581-32442698	GM12878	blood:	n/a	n/a
48	ELF1	chr11:32442404-32442732	K562	blood:	n/a	n/a
49	POLR2A	chr11:32442429-32442977	K562	blood:	n/a	n/a
50	POLR2A	chr11:32442198-32442949	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:32404442..32407230-chr11:32442115..32444001,2	K562	blood:
2	chr11:32440943..32443516-chr11:32607260..32609866,2	K562	blood:
3	chr11:32413367..32415903-chr11:32442457..32444810,2	K562	blood:
4	chr11:32431798..32437144-chr11:32439795..32446613,10	K562	blood:
5	chr11:32441708..32444112-chr11:32605234..32608760,5	K562	blood:
6	chr11:32437656..32439428-chr11:32440957..32443152,2	K562	blood:

Variant related genes	Relation type
WT1	TF binding region
ENSG00000184937	Chromatin interaction
ENSG00000149100	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10767933	0.84[ASN][1000 genomes]
rs10767935	0.84[CEU][hapmap];0.80[CHD][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs10835893	0.84[ASN][1000 genomes]
rs10835900	0.82[EUR][1000 genomes]
rs10835901	0.82[EUR][1000 genomes]
rs10835903	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10835904	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10835905	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10835906	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10835907	0.84[CEU][hapmap]
rs11031754	0.85[JPT][hapmap]
rs11031769	0.82[EUR][1000 genomes]
rs11031770	0.81[EUR][1000 genomes]
rs11824258	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12290546	0.88[ASN][1000 genomes]
rs16754	0.88[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16923242	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs1799937	0.89[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2234587	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2295081	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2295082	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301250	0.82[CHD][hapmap]
rs2900741	0.83[LWK][hapmap]
rs3809060	0.81[CHD][hapmap]
rs3809061	0.82[CHD][hapmap]
rs3818055	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs3858440	0.82[EUR][1000 genomes]
rs3858441	0.84[CEU][hapmap];0.80[CHD][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs3858442	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3858443	0.82[EUR][1000 genomes]
rs3901671	0.84[CEU][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs3930513	0.82[CHD][hapmap]
rs5030201	0.94[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5030203	0.82[JPT][hapmap]
rs5030207	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5030218	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5030317	0.94[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs5030320	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs6484574	0.84[ASN][1000 genomes]
rs6484575	0.84[ASN][1000 genomes]
rs6484576	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6484577	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7107082	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7108339	0.82[EUR][1000 genomes]
rs7110547	0.81[CHD][hapmap]
rs7115190	0.96[ASN][1000 genomes]
rs7116462	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7125543	0.82[EUR][1000 genomes]
rs7125816	0.82[EUR][1000 genomes]
rs7938016	0.84[CEU][hapmap];0.80[CHD][hapmap];0.87[MEX][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1038188	chr11:32410305-32449799	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3858445	PRR5L	cis	cerebellum	SCAN
rs3858445	TCP11L1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32438800-32447800	Weak transcription	Ovary	ovary
2	chr11:32440000-32444400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:32440800-32448400	Enhancers	Primary hematopoietic stem cells	blood
4	chr11:32441000-32443400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:32441800-32442800	Flanking Active TSS	Dnd41	blood
6	chr11:32441800-32443800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:32441800-32444000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:32441800-32444400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:32442000-32443000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:32442000-32443600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:32442000-32443800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr11:32442000-32443800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:32442000-32443800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr11:32442000-32444000	Enhancers	Primary T cells from cord blood	blood
15	chr11:32442200-32442800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:32442200-32442800	Enhancers	HSMM	muscle
17	chr11:32442200-32443000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr11:32442200-32443400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:32442200-32443600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:32442200-32443600	Enhancers	Left Ventricle	heart
21	chr11:32442200-32443800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr11:32442200-32443800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr11:32442200-32444000	Enhancers	Thymus	Thymus
24	chr11:32442200-32444400	Enhancers	HSMMtube	muscle
25	chr11:32442400-32442800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr11:32442400-32442800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr11:32442400-32442800	Flanking Active TSS	Fetal Thymus	thymus
28	chr11:32442400-32442800	Enhancers	Right Ventricle	heart
29	chr11:32442400-32443000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
30	chr11:32442400-32443000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr11:32442400-32443000	Enhancers	HMEC	breast
32	chr11:32442400-32443200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr11:32442400-32443400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr11:32442400-32443400	Enhancers	Right Atrium	heart
35	chr11:32442400-32444000	Enhancers	Fetal Heart	heart
36	chr11:32442600-32442800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr11:32442600-32442800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
38	chr11:32442600-32443000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:32442600-32443200	Enhancers	Fetal Kidney	kidney
40	chr11:32442600-32443200	Enhancers	GM12878-XiMat	blood
41	chr11:32442600-32443800	Transcr. at gene 5' and 3'	K562	blood

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