Variant report

Variant	rs11163977
Chromosome Location	chr1:84944940-84944941
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	POLR2A	chr1:84944854-84945078	A549	lung:	n/a	n/a
2	GABPA	chr1:84944220-84945464	HL-60	blood:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
3	POLR2A	chr1:84944696-84945450	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:84944751-84945476	H1-neurons	neurons:	n/a	n/a
5	YY1	chr1:84944790-84945264	A549	lung:	n/a	chr1:84945207-84945218
6	MXI1	chr1:84944409-84946625	SK-N-SH	brain:	n/a	n/a
7	TBL1XR1	chr1:84944686-84945457	K562	blood:	n/a	n/a
8	CHD1	chr1:84944872-84945194	GM12878	blood:	n/a	n/a
9	NANOG	chr1:84944638-84945134	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr1:84944929-84945603	Hela-S3	cervix:	n/a	n/a
11	UBTF	chr1:84944718-84945517	K562	blood:	n/a	n/a
12	CEBPB	chr1:84944837-84945155	ECC-1	luminal epithelium:	n/a	n/a
13	MAZ	chr1:84944773-84945501	Hela-S3	cervix:	n/a	chr1:84945328-84945339 chr1:84945327-84945336 chr1:84945201-84945211 chr1:84945330-84945339 chr1:84945331-84945338 chr1:84945327-84945342
14	MTA3	chr1:84944478-84945414	GM12878	blood:	n/a	n/a
15	TRIM28	chr1:84944550-84945315	K562	blood:	n/a	n/a
16	POLR2A	chr1:84944679-84945555	GM12892	blood:	n/a	n/a
17	GABPA	chr1:84944367-84945550	A549	lung:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
18	TAF1	chr1:84944733-84945558	SK-N-SH	brain:	n/a	n/a
19	IRF1	chr1:84944654-84945845	K562	blood:	n/a	chr1:84944926-84944946
20	POLR2A	chr1:84944669-84945464	HCT-116	colon:	n/a	n/a
21	GTF2F1	chr1:84944787-84945279	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:84944563-84945635	GM19099	blood:	n/a	n/a
23	POLR2A	chr1:84944665-84945407	U87	brain:	n/a	n/a
24	FOS	chr1:84944871-84945095	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr1:84944659-84945759	MCF10A-Er-Src	breast:	n/a	n/a
26	SETDB1	chr1:84944465-84945164	U2OS	brain:	n/a	n/a
27	ETS1	chr1:84944705-84945306	GM12878	blood:	n/a	chr1:84944885-84944894 chr1:84944886-84944896 chr1:84944885-84944894
28	BRCA1	chr1:84944796-84945516	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr1:84944745-84946041	PANC-1	pancreas:	n/a	n/a
30	YY1	chr1:84944687-84945354	H1-hESC	embryonic stem cell:	n/a	chr1:84945207-84945218
31	TBP	chr1:84944662-84945593	Hela-S3	cervix:	n/a	n/a
32	ELF1	chr1:84944637-84945441	SK-N-SH	brain:	n/a	chr1:84944884-84944893 chr1:84944883-84944894 chr1:84944883-84944894
33	YY1	chr1:84944599-84945570	SK-N-SH	brain:	n/a	chr1:84945207-84945218
34	POLR2A	chr1:84944682-84945535	GM12892	blood:	n/a	n/a
35	POLR2A	chr1:84944740-84945404	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:84944551-84945638	GM12878	blood:	n/a	n/a
37	MYC	chr1:84944714-84945540	K562	blood:	n/a	chr1:84945328-84945339 chr1:84945327-84945336 chr1:84945201-84945211 chr1:84945330-84945339 chr1:84945331-84945338 chr1:84945327-84945342 chr1:84945329-84945339
38	TAF1	chr1:84944775-84945369	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr1:84944761-84945493	MCF-7	breast:	n/a	n/a
40	POLR2A	chr1:84944524-84945623	SK-N-MC	brain:	n/a	n/a
41	MYC	chr1:84944477-84945953	K562	blood:	n/a	chr1:84945328-84945339 chr1:84945327-84945336 chr1:84945201-84945211 chr1:84945330-84945339 chr1:84945331-84945338 chr1:84945327-84945342 chr1:84945329-84945339
42	ELF1	chr1:84944690-84945115	K562	blood:	n/a	chr1:84944884-84944893 chr1:84944883-84944894 chr1:84944883-84944894
43	CEBPB	chr1:84944653-84945200	A549	lung:	n/a	n/a
44	POLR2A	chr1:84944701-84945513	Gliobla	brain:	n/a	n/a
45	ATF2	chr1:84944697-84945150	H1-hESC	embryonic stem cell:	n/a	n/a
46	REST	chr1:84944589-84945368	A549	lung:	n/a	n/a
47	MAX	chr1:84944782-84945611	MCF-7	breast:	n/a	chr1:84945328-84945339 chr1:84945327-84945336 chr1:84945201-84945211 chr1:84945330-84945339 chr1:84945331-84945338 chr1:84945327-84945342 chr1:84945329-84945339
48	ATF2	chr1:84944559-84945474	GM12878	blood:	n/a	n/a
49	TAF1	chr1:84944725-84945245	MCF-7	breast:	n/a	n/a
50	SP1	chr1:84944664-84945302	A549	lung:	n/a	chr1:84945196-84945210 chr1:84945199-84945211

No.	Distal block	Cell Line	Cell type
1	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
2	chr1:84944342..84945178-chr1:114354948..114355466,2	Hela-S3	cervix:
3	chr1:84765283..84767308-chr1:84944913..84946542,2	K562	blood:
4	chr1:84944714..84945366-chr15:68569938..68570534,2	Hela-S3	cervix:
5	chr1:84943714..84946459-chr1:85038706..85040687,2	K562	blood:
6	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
7	chr1:84765808..84767323-chr1:84944913..84947326,2	K562	blood:
8	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:

Variant related genes	Relation type
RPF1	TF binding region
ENSG00000260657	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000169018	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000203943	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000231128	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10874450	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11163978	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11163983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11163984	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11163989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11163995	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11163997	1.00[EUR][1000 genomes]
rs11163998	1.00[YRI][hapmap]
rs12067077	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075688	0.85[ASW][hapmap];1.00[YRI][hapmap]
rs12077012	1.00[EUR][1000 genomes]
rs12092954	0.82[EUR][1000 genomes]
rs12093101	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12125825	1.00[CEU][hapmap]
rs12129197	1.00[CEU][hapmap]
rs12134893	0.95[EUR][1000 genomes]
rs12137560	0.95[EUR][1000 genomes]
rs12141175	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12144912	0.95[EUR][1000 genomes]
rs1803276	0.85[ASW][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11163977	RPF1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84944000-84945000	ZNF genes & repeats	Placenta	Placenta
2	chr1:84944000-84945800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:84944200-84945000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:84944200-84945200	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:84944200-84945400	Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:84944200-84945800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr1:84944200-84946000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr1:84944200-84946200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:84944200-84946200	Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:84944200-84946200	Active TSS	A549	lung
11	chr1:84944200-84946400	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:84944400-84945000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:84944400-84945000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:84944400-84945200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
15	chr1:84944400-84945400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:84944400-84945800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:84944400-84945800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:84944400-84945800	Active TSS	Liver	Liver
19	chr1:84944400-84945800	Active TSS	Brain Substantia Nigra	brain
20	chr1:84944400-84945800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr1:84944400-84945800	Active TSS	Fetal Brain Male	brain
22	chr1:84944400-84945800	Active TSS	Left Ventricle	heart
23	chr1:84944400-84945800	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:84944400-84945800	Active TSS	NH-A	brain
25	chr1:84944400-84945800	Active TSS	Osteobl	bone
26	chr1:84944400-84946000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:84944400-84946000	Active TSS	Ovary	ovary
28	chr1:84944400-84946000	Active TSS	Stomach Mucosa	stomach
29	chr1:84944400-84946200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:84944400-84946200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:84944400-84946200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:84944400-84946200	Active TSS	Colonic Mucosa	Colon
33	chr1:84944400-84946200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr1:84944400-84946200	Active TSS	Hela-S3	cervix
35	chr1:84944400-84946200	Active TSS	HSMM	muscle
36	chr1:84944400-84946200	Active TSS	HSMMtube	muscle
37	chr1:84944400-84946400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:84944400-84946400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:84944400-84946400	Active TSS	NHLF	lung
40	chr1:84944400-84946600	Active TSS	Psoas Muscle	Psoas
41	chr1:84944400-84946600	Active TSS	NHDF-Ad	bronchial
42	chr1:84944400-84947000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:84944600-84945000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:84944600-84945000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:84944600-84945000	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr1:84944600-84945400	Active TSS	Primary B cells from cord blood	blood
47	chr1:84944600-84945600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:84944600-84945600	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr1:84944600-84945600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:84944600-84945600	Active TSS	Thymus	Thymus

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