Variant report

Variant	rs2298999
Chromosome Location	chr4:110911907-110911908
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	FOXM1	chr4:110911498-110912527	GM12878	blood:	n/a	n/a
2	NFATC1	chr4:110911629-110912472	GM12878	blood:	n/a	n/a
3	EP300	chr4:110911492-110912405	GM12878	blood:	n/a	n/a
4	CEBPB	chr4:110911628-110912461	GM12878	blood:	n/a	n/a
5	YY1	chr4:110911779-110912009	GM12892	blood:	n/a	n/a
6	POU2F2	chr4:110911721-110912298	GM12891	blood:	n/a	n/a
7	PAX5	chr4:110911789-110912047	GM12878	blood:	n/a	n/a
8	MTA3	chr4:110911611-110912319	GM12878	blood:	n/a	n/a
9	PAX5	chr4:110911755-110912043	GM12878	blood:	n/a	n/a
10	IRF4	chr4:110911618-110912360	GM12878	blood:	n/a	n/a
11	ELF1	chr4:110911618-110912328	GM12878	blood:	n/a	n/a
12	ATF2	chr4:110911553-110912468	GM12878	blood:	n/a	n/a
13	ZNF143	chr4:110911774-110912340	GM12878	blood:	n/a	n/a
14	USF1	chr4:110911687-110911933	GM12878	blood:	n/a	n/a
15	STAT5A	chr4:110911484-110912347	GM12878	blood:	n/a	chr4:110912218-110912229 chr4:110911553-110911561 chr4:110911713-110911724
16	BCLAF1	chr4:110911596-110912463	GM12878	blood:	n/a	chr4:110912220-110912229 chr4:110911729-110911736
17	MAX	chr4:110911608-110912093	GM12878	blood:	n/a	chr4:110911645-110911654
18	PML	chr4:110911708-110912275	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:110911615-110912248	GM12892	blood:	n/a	n/a
20	SP1	chr4:110911673-110912305	GM12878	blood:	n/a	n/a
21	STAT5A	chr4:110911714-110912343	GM12878	blood:	n/a	chr4:110912218-110912229
22	BHLHE40	chr4:110911328-110912385	GM12878	blood:	n/a	n/a
23	NFIC	chr4:110911583-110912522	GM12878	blood:	n/a	n/a
24	TCF3	chr4:110911622-110912401	GM12878	blood:	n/a	n/a
25	YY1	chr4:110911770-110911994	K562	blood:	n/a	n/a
26	MAZ	chr4:110911824-110912389	GM12878	blood:	n/a	n/a
27	SP1	chr4:110911656-110912306	GM12878	blood:	n/a	n/a
28	EBF1	chr4:110911839-110912322	GM12878	blood:	n/a	n/a
29	YY1	chr4:110911624-110912086	GM12878	blood:	n/a	n/a
30	STAT1	chr4:110911653-110912187	GM12878	blood:	n/a	chr4:110911713-110911724
31	POU2F2	chr4:110911593-110912316	GM12878	blood:	n/a	chr4:110911593-110911615
32	EP300	chr4:110911612-110912412	GM12878	blood:	n/a	n/a
33	RUNX3	chr4:110911254-110912474	GM12878	blood:	n/a	chr4:110911492-110911501 chr4:110911492-110911501
34	FOXM1	chr4:110911640-110912476	GM12878	blood:	n/a	n/a
35	SPI1	chr4:110911333-110912760	GM12878	blood:	n/a	chr4:110912713-110912720
36	REST	chr4:110911824-110912332	Hela-S3	cervix:	n/a	n/a
37	RELA	chr4:110911487-110912656	GM12878	blood:	n/a	n/a
38	RCOR1	chr4:110911305-110912640	GM12878	blood:	n/a	n/a
39	BCL11A	chr4:110911732-110912304	GM12878	blood:	n/a	chr4:110912220-110912229
40	BATF	chr4:110911728-110912363	GM12878	blood:	n/a	n/a
41	TCF3	chr4:110911738-110912337	GM12878	blood:	n/a	n/a
42	WRNIP1	chr4:110911591-110912257	GM12878	blood:	n/a	n/a
43	TCF12	chr4:110911739-110912296	GM12878	blood:	n/a	n/a
44	PAX5	chr4:110911541-110912342	GM12878	blood:	n/a	chr4:110911555-110911564 chr4:110912220-110912229
45	SPI1	chr4:110911664-110912352	GM12891	blood:	n/a	n/a
46	IKZF1	chr4:110911475-110912684	GM12878	blood:	n/a	n/a
47	BCL11A	chr4:110911692-110912331	GM12878	blood:	n/a	chr4:110912220-110912229 chr4:110911729-110911736
48	SPI1	chr4:110911700-110912359	GM12878	blood:	n/a	n/a
49	MTA3	chr4:110911575-110912438	GM12878	blood:	n/a	n/a
50	USF2	chr4:110911489-110912146	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110910332..110912900-chr4:111091767..111093737,2	K562	blood:
2	chr4:110905512..110907567-chr4:110910504..110912580,2	K562	blood:

Variant related genes	Relation type
RNU6-35P	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11098057	0.81[CEU][hapmap]
rs2074390	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2237049	0.81[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap]
rs2237051	0.81[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2237052	0.82[JPT][hapmap]
rs2237053	0.80[CEU][hapmap];0.84[YRI][hapmap]
rs6533485	0.87[JPT][hapmap]
rs6824594	0.81[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs7692976	0.82[JPT][hapmap]
rs882471	0.81[CEU][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298999	RRH	cis	cerebellum	SCAN
rs2298999	GAR1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110895000-110928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:110901000-110929600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:110901400-110920800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:110906800-110920800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:110907000-110932400	Weak transcription	Psoas Muscle	Psoas
6	chr4:110907800-110927400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:110908600-110916200	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:110909600-110912000	Enhancers	HMEC	breast
9	chr4:110909600-110913800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:110910200-110920400	Weak transcription	Fetal Intestine Small	intestine
11	chr4:110910400-110935200	Weak transcription	Pancreas	Pancrea
12	chr4:110910600-110929800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:110910800-110926800	Weak transcription	Fetal Heart	heart
14	chr4:110911000-110912000	Enhancers	NHEK	skin
15	chr4:110911200-110912200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:110911200-110912800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:110911200-110913400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr4:110911400-110912200	Flanking Active TSS	GM12878-XiMat	blood
19	chr4:110911600-110912000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:110911600-110912800	Enhancers	Esophagus	oesophagus
21	chr4:110911800-110912200	Enhancers	Fetal Thymus	thymus
22	chr4:110911800-110917800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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