Variant report

Variant	rs72698116
Chromosome Location	chr1:154380934-154380935
allele	A/G
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	RXRA	chr1:154380924-154381262	HepG2	liver:	n/a	n/a
2	SMC3	chr1:154380878-154381222	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:154380400-154381355	HepG2	liver:	n/a	chr1:154380796-154380811 chr1:154381107-154381119
4	HNF4A	chr1:154380835-154381206	HepG2	liver:	n/a	n/a
5	FOXA1	chr1:154380415-154380954	T-47D	breast:	n/a	chr1:154380796-154380811
6	NR2F2	chr1:154380757-154381473	HepG2	liver:	n/a	n/a
7	RUNX3	chr1:154380719-154381163	GM12878	blood:	n/a	n/a
8	MTA3	chr1:154380682-154381211	GM12878	blood:	n/a	n/a
9	NFIC	chr1:154380874-154381320	HepG2	liver:	n/a	n/a
10	HEY1	chr1:154380814-154381234	HepG2	liver:	n/a	n/a
11	MBD4	chr1:154380867-154381294	HepG2	liver:	n/a	n/a
12	FOXA2	chr1:154380921-154381243	HepG2	liver:	n/a	chr1:154381107-154381119
13	CEBPB	chr1:154379495-154380979	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:154380911-154381356	HepG2	liver:	n/a	n/a
15	HDAC2	chr1:154380820-154381237	HepG2	liver:	n/a	n/a
16	TEAD4	chr1:154380863-154381328	HepG2	liver:	n/a	n/a
17	CHD1	chr1:154376982-154381411	IMR90	lung:	n/a	n/a
18	FOXA1	chr1:154380594-154381257	T-47D	breast:	n/a	chr1:154380796-154380811 chr1:154381107-154381119
19	FOXA1	chr1:154380640-154381335	HepG2	liver:	n/a	chr1:154380796-154380811 chr1:154381107-154381119
20	SPI1	chr1:154380508-154381249	HL-60	blood:	n/a	chr1:154381180-154381193 chr1:154381013-154381020 chr1:154381010-154381023
21	NFIC	chr1:154379455-154381177	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:154377502-154382614	MCF10A-Er-Src	breast:	n/a	n/a
23	MXI1	chr1:154377096-154381012	IMR90	lung:	n/a	n/a
24	RUNX3	chr1:154379322-154381160	GM12878	blood:	n/a	n/a
25	PML	chr1:154378788-154381090	GM12878	blood:	n/a	n/a
26	EBF1	chr1:154380835-154381118	GM12878	blood:	n/a	n/a
27	SPI1	chr1:154380811-154381075	GM12878	blood:	n/a	chr1:154381013-154381020 chr1:154381010-154381023
28	POLR2A	chr1:154377097-154381240	GM18505	blood:	n/a	n/a
29	EP300	chr1:154380866-154381336	HepG2	liver:	n/a	chr1:154381102-154381112
30	POLR2A	chr1:154377291-154381193	IMR90	lung:	n/a	n/a
31	POLR2A	chr1:154379563-154381110	GM12891	blood:	n/a	n/a
32	EP300	chr1:154380734-154381276	HepG2	liver:	n/a	chr1:154381102-154381112
33	EP300	chr1:154380882-154381306	HepG2	liver:	n/a	chr1:154381102-154381112
34	RELA	chr1:154379636-154381225	GM18505	blood:	n/a	n/a
35	RCOR1	chr1:154376980-154381066	IMR90	lung:	n/a	n/a
36	RELA	chr1:154379761-154381086	GM19099	blood:	n/a	n/a
37	STAT5A	chr1:154380456-154381073	GM12878	blood:	n/a	chr1:154380919-154380931 chr1:154380459-154380471
38	RELA	chr1:154379610-154381113	GM19193	blood:	n/a	n/a
39	FOXA1	chr1:154380915-154381307	HepG2	liver:	n/a	chr1:154381107-154381119
40	SPI1	chr1:154380584-154381158	GM12891	blood:	n/a	chr1:154381013-154381020 chr1:154381010-154381023

No.	Distal block	Cell Line	Cell type
1	chr1:154376462..154378144-chr1:154380867..154382690,2	K562	blood:
2	chr1:154379631..154382392-chr20:55784816..55787372,2	MCF-7	breast:
3	chr1:154154370..154156741-chr1:154377003..154381011,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	TF binding region
ENSG00000160712	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12090237	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34806329	1.00[EUR][1000 genomes]
rs55886061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698118	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698126	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7411976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer 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 miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154377000-154381000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:154377000-154381200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:154377200-154381200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:154377400-154381200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr1:154377800-154381200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:154378000-154381200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr1:154378200-154381000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr1:154378200-154381000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:154378200-154381400	Flanking Active TSS	GM12878-XiMat	blood
10	chr1:154378200-154382600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr1:154378400-154381200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:154378600-154381000	Flanking Active TSS	NHEK	skin
13	chr1:154378800-154381000	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr1:154378800-154381000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr1:154378800-154381600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr1:154379000-154381000	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr1:154379000-154381000	Enhancers	HSMMtube	muscle
18	chr1:154379000-154381200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:154379000-154381200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr1:154379000-154381200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:154379000-154381200	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr1:154379000-154381400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:154379000-154381800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:154379000-154381800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:154379200-154381000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:154379200-154381200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:154379200-154381200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:154379200-154381200	Enhancers	Gastric	stomach
29	chr1:154379200-154381400	Enhancers	A549	lung
30	chr1:154379200-154381600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:154379200-154382000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:154379400-154381200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr1:154379400-154381200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:154379400-154381200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:154379400-154381200	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr1:154379400-154381200	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr1:154379400-154381200	Flanking Active TSS	Stomach Mucosa	stomach
38	chr1:154379400-154383000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:154379600-154381400	Flanking Active TSS	HepG2	liver
40	chr1:154379800-154381000	Enhancers	Esophagus	oesophagus
41	chr1:154379800-154381000	Enhancers	Osteobl	bone
42	chr1:154379800-154381200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr1:154379800-154381200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:154379800-154381200	Enhancers	Lung	lung
45	chr1:154379800-154381400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:154379800-154382000	Enhancers	Brain Substantia Nigra	brain
47	chr1:154379800-154382600	Enhancers	Brain Angular Gyrus	brain
48	chr1:154380000-154381200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:154380000-154381400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr1:154380000-154381400	Enhancers	Spleen	Spleen

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