Variant report

Variant	rs11158621
Chromosome Location	chr14:24743387-24743388
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	POLR2A	chr14:24743305-24743804	GM12892	blood:	n/a	n/a
2	CEBPB	chr14:24743268-24743625	K562	blood:	n/a	n/a
3	IRF4	chr14:24743184-24743778	GM12878	blood:	n/a	n/a
4	CEBPB	chr14:24743292-24743602	K562	blood:	n/a	n/a
5	EP300	chr14:24742887-24743748	GM12878	blood:	n/a	chr14:24743520-24743534
6	ATF2	chr14:24743030-24743789	GM12878	blood:	n/a	n/a
7	EBF1	chr14:24743266-24743945	GM12878	blood:	n/a	n/a
8	RUNX3	chr14:24743041-24743797	GM12878	blood:	n/a	n/a
9	STAT3	chr14:24742745-24743809	MCF10A-Er-Src	breast:	n/a	n/a
10	BHLHE40	chr14:24743324-24743798	GM12878	blood:	n/a	n/a
11	BCL11A	chr14:24743289-24743653	GM12878	blood:	n/a	n/a
12	BATF	chr14:24743196-24743695	GM12878	blood:	n/a	n/a
13	STAT5A	chr14:24743209-24743663	GM12878	blood:	n/a	n/a
14	MTA3	chr14:24743080-24743944	GM12878	blood:	n/a	n/a
15	ZEB1	chr14:24743199-24743826	GM12878	blood:	n/a	n/a
16	STAT3	chr14:24742899-24743706	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr14:24742759-24743974	MCF10A-Er-Src	breast:	n/a	chr14:24743498-24743509
18	MYC	chr14:24743277-24743925	MCF10A-Er-Src	breast:	n/a	chr14:24743449-24743458
19	POLR2A	chr14:24743269-24743522	GM12878	blood:	n/a	n/a
20	STAT3	chr14:24742800-24743917	MCF10A-Er-Src	breast:	n/a	n/a
21	GATA1	chr14:24743290-24743910	PBDE	blood:	n/a	chr14:24743693-24743700 chr14:24743688-24743704 chr14:24743693-24743700 chr14:24743691-24743701 chr14:24743693-24743700 chr14:24743522-24743532 chr14:24743691-24743700 chr14:24743686-24743707
22	PML	chr14:24743349-24743628	GM12878	blood:	n/a	chr14:24743555-24743563
23	PML	chr14:24743116-24743943	GM12878	blood:	n/a	chr14:24743555-24743563 chr14:24743634-24743642
24	FOXM1	chr14:24743192-24743846	GM12878	blood:	n/a	n/a
25	MTA3	chr14:24743102-24743962	GM12878	blood:	n/a	n/a
26	SPI1	chr14:24743312-24743767	HL-60	blood:	n/a	chr14:24743519-24743532 chr14:24743522-24743529
27	PAX5	chr14:24743304-24743565	GM12892	blood:	n/a	chr14:24743522-24743531
28	POLR2A	chr14:24743206-24743830	GM12892	blood:	n/a	n/a
29	SPI1	chr14:24743191-24743810	HL-60	blood:	n/a	chr14:24743519-24743532 chr14:24743522-24743529
30	RCOR1	chr14:24743331-24743858	K562	blood:	n/a	n/a
31	PAX5	chr14:24743299-24743635	GM12878	blood:	n/a	chr14:24743522-24743531
32	NFYB	chr14:24743333-24743597	GM12878	blood:	n/a	n/a
33	GATA1	chr14:24743189-24743869	K562	blood:	n/a	chr14:24743693-24743700 chr14:24743688-24743704 chr14:24743693-24743700 chr14:24743691-24743701 chr14:24743693-24743700 chr14:24743522-24743532 chr14:24743691-24743700 chr14:24743686-24743707
34	CCNT2	chr14:24743371-24743807	K562	blood:	n/a	n/a
35	SPI1	chr14:24743296-24743653	GM12878	blood:	n/a	chr14:24743519-24743532 chr14:24743522-24743529
36	FOXM1	chr14:24743254-24743843	GM12878	blood:	n/a	n/a
37	SPI1	chr14:24742971-24743969	GM12878	blood:	n/a	chr14:24743519-24743532 chr14:24743522-24743529
38	FOS	chr14:24742797-24743920	MCF10A-Er-Src	breast:	n/a	chr14:24743498-24743509
39	CEBPB	chr14:24743010-24743619	Hela-S3	cervix:	n/a	n/a
40	NFATC1	chr14:24743265-24743799	GM12878	blood:	n/a	n/a
41	NFIC	chr14:24743164-24743850	GM12878	blood:	n/a	n/a
42	BCL11A	chr14:24743239-24743700	GM12878	blood:	n/a	n/a
43	FOS	chr14:24743204-24743881	MCF10A-Er-Src	breast:	n/a	chr14:24743498-24743509
44	REST	chr14:24743327-24743661	Hela-S3	cervix:	n/a	n/a
45	CEBPB	chr14:24743369-24743610	GM12878	blood:	n/a	n/a
46	IRF4	chr14:24743204-24743740	GM12878	blood:	n/a	n/a
47	E2F4	chr14:24742991-24743759	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr14:24742920-24743752	MCF10A-Er-Src	breast:	n/a	chr14:24743498-24743509
49	ATF2	chr14:24743108-24743803	GM12878	blood:	n/a	n/a
50	IKZF1	chr14:24743109-24743881	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:24741150..24743790-chr14:24903528..24906094,2	K562	blood:
2	chr14:24742260..24745882-chr14:24750433..24756794,5	K562	blood:
3	chr14:24733261..24735631-chr14:24742751..24745334,2	K562	blood:
4	chr14:24680755..24686632-chr14:24737203..24743863,8	MCF-7	breast:
5	chr14:24741724..24744792-chr14:24900386..24902979,3	MCF-7	breast:
6	chr14:24655787..24658216-chr14:24740858..24744211,3	K562	blood:

Variant related genes	Relation type
RABGGTA	TF binding region
ENSG00000254505	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000260669	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000092295	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs14193	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295313	0.85[EUR][1000 genomes]
rs3940231	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982887	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729421	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941502	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941503	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11158621	RABGGTA	cis	multi-tissue	Pritchard
rs11158621	RABGGTA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24740800-24743800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr14:24740800-24743800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr14:24741000-24743400	Weak transcription	Spleen	Spleen
4	chr14:24741200-24753200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:24741200-24758800	Weak transcription	Aorta	Aorta
6	chr14:24741200-24768200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:24741400-24743400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr14:24741400-24743400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr14:24741400-24743600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr14:24741400-24743800	Enhancers	Primary hematopoietic stem cells	blood
11	chr14:24741400-24743800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr14:24741400-24743800	Enhancers	Liver	Liver
13	chr14:24741400-24744000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:24741400-24744000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:24741400-24744200	Enhancers	Primary B cells from peripheral blood	blood
16	chr14:24741400-24744600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:24741400-24744800	Enhancers	Primary B cells from cord blood	blood
18	chr14:24741400-24745200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:24741400-24745200	Enhancers	HMEC	breast
20	chr14:24741400-24746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr14:24741400-24746200	Weak transcription	Colonic Mucosa	Colon
22	chr14:24741400-24746400	Weak transcription	Right Ventricle	heart
23	chr14:24741400-24747600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr14:24741400-24747600	Weak transcription	Brain Substantia Nigra	brain
25	chr14:24741400-24748400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:24741400-24748400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:24741400-24748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr14:24741400-24748400	Weak transcription	Brain Angular Gyrus	brain
29	chr14:24741400-24748400	Weak transcription	Brain Anterior Caudate	brain
30	chr14:24741400-24748400	Weak transcription	Psoas Muscle	Psoas
31	chr14:24741400-24748400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr14:24741400-24748400	Weak transcription	HSMM	muscle
33	chr14:24741400-24748800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr14:24741400-24748800	Weak transcription	Lung	lung
35	chr14:24741400-24749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:24741400-24749800	Weak transcription	HSMMtube	muscle
37	chr14:24741400-24751800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:24741400-24752200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr14:24741400-24752200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:24741400-24757800	Weak transcription	Fetal Stomach	stomach
41	chr14:24741400-24758600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:24741400-24758800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr14:24741600-24743400	Enhancers	HepG2	liver
44	chr14:24741600-24743800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:24741600-24743800	Enhancers	Hela-S3	cervix
46	chr14:24741600-24744000	Enhancers	K562	blood
47	chr14:24741600-24744400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr14:24741600-24744800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:24741600-24744800	Weak transcription	Fetal Intestine Small	intestine
50	chr14:24741600-24745200	Enhancers	Primary T helper cells PMA-I stimulated	--

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