Variant report

Variant	rs71504690
Chromosome Location	chr9:2012403-2012404
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	TBP	chr9:2012164-2012988	GM12878	blood:	n/a	n/a
2	SP1	chr9:2012215-2012762	GM12878	blood:	n/a	n/a
3	BCLAF1	chr9:2012177-2012878	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
4	CUX1	chr9:2012364-2012997	GM12878	blood:	n/a	n/a
5	JUND	chr9:2012314-2012673	HepG2	liver:	n/a	chr9:2012493-2012501 chr9:2012493-2012500 chr9:2012492-2012501 chr9:2012493-2012502 chr9:2012491-2012502
6	TEAD4	chr9:2012133-2012546	K562	blood:	n/a	n/a
7	EP300	chr9:2012291-2012657	GM12878	blood:	n/a	chr9:2012492-2012501 chr9:2012493-2012502
8	POU2F2	chr9:2012379-2012626	GM12891	blood:	n/a	n/a
9	PML	chr9:2012295-2012763	GM12878	blood:	n/a	chr9:2012494-2012503 chr9:2012491-2012500
10	MEF2A	chr9:2012170-2012818	GM12878	blood:	n/a	n/a
11	BATF	chr9:2012231-2012720	GM12878	blood:	n/a	chr9:2012489-2012500 chr9:2012494-2012504
12	MTA3	chr9:2012150-2013006	GM12878	blood:	n/a	n/a
13	NFIC	chr9:2012049-2012971	GM12878	blood:	n/a	n/a
14	CHD2	chr9:2012223-2012805	GM12878	blood:	n/a	n/a
15	BCL11A	chr9:2012252-2012716	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
16	EBF1	chr9:2012355-2012665	GM12878	blood:	n/a	n/a
17	EBF1	chr9:2012356-2012699	GM12878	blood:	n/a	n/a
18	CEBPB	chr9:2012007-2013098	GM12878	blood:	n/a	n/a
19	RAD21	chr9:2012361-2012644	GM12878	blood:	n/a	chr9:2012545-2012558
20	IRF4	chr9:2012206-2012757	GM12878	blood:	n/a	n/a
21	NFIC	chr9:2011828-2013133	GM12878	blood:	n/a	n/a
22	NFATC1	chr9:2012112-2012984	GM12878	blood:	n/a	n/a
23	GATA2	chr9:2012203-2012535	K562	blood:	n/a	chr9:2012435-2012446
24	JUND	chr9:2012336-2012748	K562	blood:	n/a	chr9:2012493-2012501 chr9:2012493-2012500 chr9:2012678-2012685 chr9:2012492-2012501 chr9:2012493-2012502 chr9:2012491-2012502
25	EBF1	chr9:2012154-2013282	GM12878	blood:	n/a	chr9:2013083-2013092
26	RCOR1	chr9:2012277-2012901	GM12878	blood:	n/a	n/a
27	FOXM1	chr9:2012102-2012950	GM12878	blood:	n/a	n/a
28	MAZ	chr9:2012309-2012880	GM12878	blood:	n/a	chr9:2012493-2012502
29	MEF2A	chr9:2012123-2012860	GM12878	blood:	n/a	n/a
30	RUNX3	chr9:2012054-2012997	GM12878	blood:	n/a	n/a
31	BCL3	chr9:2012231-2012873	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
32	PAX5	chr9:2012209-2012777	GM12878	blood:	n/a	chr9:2012462-2012471
33	PML	chr9:2012100-2013084	GM12878	blood:	n/a	chr9:2012494-2012503 chr9:2012491-2012500
34	ATF3	chr9:2012355-2012584	K562	blood:	n/a	n/a
35	IRF4	chr9:2012135-2012731	GM12878	blood:	n/a	n/a
36	NFATC1	chr9:2012181-2012907	GM12878	blood:	n/a	n/a
37	BCL11A	chr9:2012367-2012638	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
38	BCLAF1	chr9:2012286-2012871	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
39	TBL1XR1	chr9:2012200-2012845	GM12878	blood:	n/a	n/a
40	MAX	chr9:2012218-2012608	GM12878	blood:	n/a	chr9:2012493-2012502
41	FOXM1	chr9:2012051-2013013	GM12878	blood:	n/a	n/a
42	SMC3	chr9:2012376-2012866	GM12878	blood:	n/a	n/a
43	BHLHE40	chr9:2012316-2012820	GM12878	blood:	n/a	n/a
44	RUNX3	chr9:2012194-2012872	GM12878	blood:	n/a	n/a
45	JUN	chr9:2012384-2012605	HepG2	liver:	n/a	chr9:2012493-2012501 chr9:2012493-2012500 chr9:2012492-2012501 chr9:2012493-2012502
46	STAT5A	chr9:2012142-2012730	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
47	STAT5A	chr9:2012198-2012747	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
48	STAT1	chr9:2012284-2012769	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501
49	BATF	chr9:2012130-2012836	GM12878	blood:	n/a	chr9:2012489-2012500 chr9:2012494-2012504
50	STAT3	chr9:2012145-2012956	GM12878	blood:	n/a	chr9:2012493-2012502 chr9:2012492-2012501

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2006630..2009336-chr9:2010265..2012993,2	K562	blood:
2	chr9:1981753..1984012-chr9:2012148..2014267,2	K562	blood:

Variant related genes	Relation type
SMARCA2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10757112	0.96[ASN][1000 genomes]
rs4741636	0.87[ASN][1000 genomes]
rs7032161	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7040790	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1021712	chr9:1647840-2216839	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv539921	chr9:1647840-2216839	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
5	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv831493	chr9:1885733-2074135	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv892047	chr9:1888703-2018825	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv892048	chr9:1888703-2177391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1021158	chr9:1963930-2040728	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv892052	chr9:1980819-2072470	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv2830420	chr9:1998911-2119702	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2005800-2014200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:2009200-2013600	Weak transcription	Right Atrium	heart
3	chr9:2009400-2013600	Weak transcription	Liver	Liver
4	chr9:2011600-2014600	Weak transcription	Lung	lung
5	chr9:2012000-2014200	Flanking Active TSS	GM12878-XiMat	blood
6	chr9:2012400-2012600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr9:2012400-2012600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:2012400-2012600	Enhancers	K562	blood

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