Variant report

Variant	rs2233913
Chromosome Location	chr9:115983216-115983217
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	CHD2	chr9:115983003-115984216	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr9:115983182-115984563	K562	blood:	n/a	n/a
3	ELF1	chr9:115983145-115983761	HepG2	liver:	n/a	chr9:115983608-115983617 chr9:115983368-115983377
4	POU2F2	chr9:115983213-115983926	GM12878	blood:	n/a	chr9:115983692-115983705 chr9:115983809-115983821
5	POLR2A	chr9:115983160-115984205	MCF-7	breast:	n/a	n/a
6	TAF1	chr9:115983172-115984147	HepG2	liver:	n/a	n/a
7	ELF1	chr9:115983147-115984271	GM12878	blood:	n/a	chr9:115983608-115983617 chr9:115984105-115984117 chr9:115983368-115983377
8	MAX	chr9:115982891-115985189	Hela-S3	cervix:	n/a	chr9:115983813-115983823
9	TCF12	chr9:115982982-115984412	A549	lung:	n/a	n/a
10	MXI1	chr9:115981145-115984347	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:115983152-115985096	Hela-S3	cervix:	n/a	n/a
12	GABPA	chr9:115983165-115984138	K562	blood:	n/a	n/a
13	POLR2A	chr9:115982795-115984928	Hela-S3	cervix:	n/a	n/a
14	ELF1	chr9:115982754-115984112	MCF-7	breast:	n/a	chr9:115983608-115983617 chr9:115983368-115983377
15	PML	chr9:115981826-115984110	GM12878	blood:	n/a	chr9:115983963-115983971
16	FOXM1	chr9:115983052-115983754	GM12878	blood:	n/a	n/a
17	TEAD4	chr9:115982956-115984076	K562	blood:	n/a	n/a
18	TEAD4	chr9:115983055-115984121	ECC-1	luminal epithelium:	n/a	n/a
19	SIN3A	chr9:115982839-115984504	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr9:115983139-115984209	ECC-1	luminal epithelium:	n/a	n/a
21	TEAD4	chr9:115983128-115983856	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr9:115982918-115984226	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr9:115983036-115984989	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr9:115982995-115984233	MCF-7	breast:	n/a	n/a
25	MAX	chr9:115982891-115984039	K562	blood:	n/a	chr9:115983813-115983823
26	KAP1	chr9:115982993-115984095	HEK293	kidney:	n/a	chr9:115983963-115983971
27	REST	chr9:115982652-115984595	H1-neurons	neurons:	n/a	chr9:115983838-115983851
28	POLR2A	chr9:115983171-115984138	GM12892	blood:	n/a	n/a
29	MAZ	chr9:115982930-115984275	Hela-S3	cervix:	n/a	chr9:115983813-115983823
30	MAZ	chr9:115983131-115984170	GM12878	blood:	n/a	chr9:115983813-115983823
31	POLR2A	chr9:115981373-115984128	GM12891	blood:	n/a	n/a
32	TBP	chr9:115982870-115984081	K562	blood:	n/a	n/a
33	TAF1	chr9:115983207-115984108	PFSK-1	brain:	n/a	n/a
34	TEAD4	chr9:115983185-115983558	H1-hESC	embryonic stem cell:	n/a	n/a
35	RELA	chr9:115982122-115984391	GM18951	blood:	n/a	n/a
36	MAZ	chr9:115983047-115985166	IMR90	lung:	n/a	chr9:115983813-115983823
37	NR2F2	chr9:115982813-115984988	K562	blood:	n/a	n/a
38	POLR2A	chr9:115983164-115984139	K562	blood:	n/a	n/a
39	TBP	chr9:115982984-115985238	Hela-S3	cervix:	n/a	n/a
40	RUNX3	chr9:115981378-115983926	GM12878	blood:	n/a	n/a
41	GTF3C2	chr9:115982955-115983402	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr9:115983117-115983684	GM12878	blood:	n/a	n/a
43	GATA3	chr9:115983158-115984056	A549	lung:	n/a	chr9:115983235-115983243
44	MAX	chr9:115983197-115984199	A549	lung:	n/a	chr9:115983813-115983823
45	ELF1	chr9:115983044-115983968	MCF-7	breast:	n/a	chr9:115983608-115983617 chr9:115983368-115983377
46	POLR2A	chr9:115982203-115984095	GM18505	blood:	n/a	n/a
47	MAX	chr9:115983178-115984179	ECC-1	luminal epithelium:	n/a	chr9:115983813-115983823
48	POLR2A	chr9:115983028-115984546	H1-hESC	embryonic stem cell:	n/a	n/a
49	MXI1	chr9:115981681-115985060	SK-N-SH	brain:	n/a	n/a
50	CUX1	chr9:115983194-115983586	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
2	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
3	chr9:115968725..115971196-chr9:115981878..115984279,2	MCF-7	breast:
4	chr9:115981081..115983502-chr9:115983537..115987172,3	MCF-7	breast:
5	chr9:115981852..115985156-chr9:116171660..116173942,3	MCF-7	breast:
6	chr9:115982263..115984734-chr9:116036359..116038354,4	MCF-7	breast:
7	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:

Variant related genes	Relation type
SLC31A1	TF binding region
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10123780	1.00[CHB][hapmap]
rs10513190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794908	0.81[GIH][hapmap]
rs12337498	1.00[CHB][hapmap]
rs17763351	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571	1.00[LWK][hapmap]
rs3087548	1.00[CHB][hapmap]
rs3810917	1.00[CHB][hapmap]
rs3810918	1.00[CHB][hapmap]
rs3827672	0.81[GIH][hapmap]
rs4480181	0.81[GIH][hapmap];0.92[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2233913	SDS	trans	parietal	SCAN
rs2233913	ZNF483	cis	cerebellum	SCAN
rs2233913	CDC26	cis	cerebellum	SCAN
rs2233913	CDC26	cis	parietal	SCAN
rs2233913	PRPF4	cis	Thyroid	GTEx
rs2233913	ROD1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115981200-115983400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr9:115981200-115985600	Active TSS	GM12878-XiMat	blood
3	chr9:115981400-115983400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:115981800-115983400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr9:115981800-115983400	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr9:115981800-115983400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:115982000-115984800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:115982000-115985000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr9:115982000-115985000	Active TSS	Aorta	Aorta
10	chr9:115982200-115985000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:115982200-115985200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:115982200-115985400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:115982200-115985600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:115982400-115983400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr9:115982400-115984400	Active TSS	Fetal Muscle Trunk	muscle
16	chr9:115982400-115984400	Active TSS	Left Ventricle	heart
17	chr9:115982400-115984600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr9:115982400-115984600	Active TSS	NHDF-Ad	bronchial
19	chr9:115982400-115984800	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr9:115982400-115985000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr9:115982400-115985200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:115982400-115985400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr9:115982400-115985400	Active TSS	HSMMtube	muscle
24	chr9:115982600-115983400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr9:115982600-115983400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr9:115982600-115983400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:115982600-115984000	Active TSS	Thymus	Thymus
28	chr9:115982600-115984400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:115982600-115984400	Active TSS	K562	blood
30	chr9:115982600-115984600	Active TSS	H1 Cell Line	embryonic stem cell
31	chr9:115982600-115984600	Active TSS	Esophagus	oesophagus
32	chr9:115982600-115984600	Active TSS	Ovary	ovary
33	chr9:115982600-115984600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr9:115982600-115984800	Active TSS	Psoas Muscle	Psoas
35	chr9:115982600-115984800	Active TSS	A549	lung
36	chr9:115982600-115984800	Active TSS	NHLF	lung
37	chr9:115982600-115985000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:115982600-115985600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:115982800-115984000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr9:115982800-115984200	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr9:115982800-115984200	Active TSS	Spleen	Spleen
42	chr9:115982800-115984200	Active TSS	Dnd41	blood
43	chr9:115982800-115984400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr9:115982800-115984400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:115982800-115984400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr9:115982800-115984400	Active TSS	Gastric	stomach
47	chr9:115982800-115984400	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr9:115982800-115984400	Active TSS	HSMM	muscle
49	chr9:115982800-115984600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:115982800-115984600	Active TSS	Small Intestine	intestine

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