Variant report

Variant	rs72948416
Chromosome Location	chr1:84944508-84944509
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	GABPA	chr1:84944220-84945464	HL-60	blood:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
2	MXI1	chr1:84944409-84946625	SK-N-SH	brain:	n/a	n/a
3	MTA3	chr1:84944478-84945414	GM12878	blood:	n/a	n/a
4	GABPA	chr1:84944367-84945550	A549	lung:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
5	SETDB1	chr1:84944465-84945164	U2OS	brain:	n/a	n/a
6	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
7	PML	chr1:84944498-84945608	GM12878	blood:	n/a	n/a
8	GABPA	chr1:84944374-84945619	SK-N-SH	brain:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
9	GABPA	chr1:84944415-84945430	H1-hESC	embryonic stem cell:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
10	POLR2A	chr1:84944389-84945755	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr1:84944352-84944547	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:84944462-84945994	PANC-1	pancreas:	n/a	n/a
13	GABPA	chr1:84944476-84945471	MCF-7	breast:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
14	GABPA	chr1:84944233-84945704	A549	lung:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
15	RELA	chr1:84944495-84945661	GM15510	blood:	n/a	n/a
16	HCFC1	chr1:84944333-84946183	Hela-S3	cervix:	n/a	n/a
17	NR2C2	chr1:84944196-84945416	GM12878	blood:	n/a	chr1:84944883-84944890
18	MAX	chr1:84944328-84945774	HCT-116	colon:	n/a	chr1:84945328-84945339 chr1:84945327-84945336 chr1:84945201-84945211 chr1:84945330-84945339 chr1:84945331-84945338 chr1:84945327-84945342 chr1:84945329-84945339
19	NR2C2	chr1:84944328-84945549	Hela-S3	cervix:	n/a	chr1:84944883-84944890
20	ELF1	chr1:84944500-84945543	HCT-116	colon:	n/a	chr1:84944884-84944893 chr1:84944883-84944894 chr1:84944883-84944894
21	MTA3	chr1:84944483-84945757	GM12878	blood:	n/a	n/a
22	GABPA	chr1:84944345-84945646	SK-N-SH	brain:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
23	GABPA	chr1:84944209-84945846	MCF-7	breast:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
24	ELF1	chr1:84944422-84945495	HCT-116	colon:	n/a	chr1:84944884-84944893 chr1:84944883-84944894 chr1:84944883-84944894
25	CBX3	chr1:84944362-84945199	K562	blood:	n/a	n/a
26	SREBP2	chr1:84944018-84946811	GM12878	blood:	n/a	n/a
27	GABPA	chr1:84944414-84945415	HL-60	blood:	n/a	chr1:84945217-84945228 chr1:84945219-84945228
28	TCF12	chr1:84944414-84945403	A549	lung:	n/a	n/a
29	POLR2A	chr1:84944412-84945871	GM12891	blood:	n/a	n/a
30	ELF1	chr1:84944499-84945494	SK-N-SH	brain:	n/a	chr1:84944884-84944893 chr1:84944883-84944894 chr1:84944883-84944894
31	SETDB1	chr1:84944487-84945554	K562	blood:	n/a	chr1:84945218-84945227
32	CBX3	chr1:84944313-84945655	K562	blood:	n/a	n/a

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	chr1:84943714..84946459-chr1:85038706..85040687,2	K562	blood:
4	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
5	chr1:84920904..84923414-chr1:84941843..84944839,2	K562	blood:
6	chr1:84928129..84930451-chr1:84943094..84944929,2	MCF-7	breast:

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

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11163973	0.96[ASN][1000 genomes]
rs11163974	0.88[ASN][1000 genomes]
rs11163975	0.96[ASN][1000 genomes]
rs11163976	0.96[ASN][1000 genomes]
rs11163982	0.88[ASN][1000 genomes]
rs11163985	0.88[ASN][1000 genomes]
rs11163987	0.88[ASN][1000 genomes]
rs13093	0.88[ASN][1000 genomes]
rs17110164	0.88[ASN][1000 genomes]
rs17110485	0.88[ASN][1000 genomes]
rs17110590	0.88[ASN][1000 genomes]
rs3768247	0.81[ASN][1000 genomes]
rs56876287	0.88[ASN][1000 genomes]
rs6658034	0.96[ASN][1000 genomes]
rs6658974	0.88[ASN][1000 genomes]
rs6662644	0.88[ASN][1000 genomes]
rs6662683	0.88[ASN][1000 genomes]
rs6666052	0.96[ASN][1000 genomes]
rs6666572	0.96[ASN][1000 genomes]
rs6668752	0.88[ASN][1000 genomes]
rs6676502	0.84[ASN][1000 genomes]
rs6684882	0.88[ASN][1000 genomes]
rs6701280	0.88[ASN][1000 genomes]
rs6704452	0.88[ASN][1000 genomes]
rs7524576	0.88[ASN][1000 genomes]
rs7539413	0.88[ASN][1000 genomes]
rs7541850	0.81[ASN][1000 genomes]
rs7541909	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7547208	0.88[ASN][1000 genomes]
rs7551329	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555773	0.88[ASN][1000 genomes]
rs7555821	0.88[ASN][1000 genomes]

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

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84943800-84944800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
2	chr1:84944000-84945000	ZNF genes & repeats	Placenta	Placenta
3	chr1:84944000-84945800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:84944200-84944600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:84944200-84944600	Flanking Active TSS	Brain Cingulate Gyrus	brain
6	chr1:84944200-84944600	Flanking Active TSS	Colon Smooth Muscle	Colon
7	chr1:84944200-84944800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr1:84944200-84944800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:84944200-84944800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr1:84944200-84944800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:84944200-84944800	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr1:84944200-84944800	Bivalent/Poised TSS	Fetal Lung	lung
13	chr1:84944200-84944800	ZNF genes & repeats	GM12878-XiMat	blood
14	chr1:84944200-84945000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:84944200-84945200	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr1:84944200-84945400	Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr1:84944200-84945800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:84944200-84946000	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:84944200-84946200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:84944200-84946200	Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:84944200-84946200	Active TSS	A549	lung
22	chr1:84944200-84946400	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:84944400-84944600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:84944400-84944600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:84944400-84944600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:84944400-84944600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr1:84944400-84944600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
28	chr1:84944400-84944600	Enhancers	Primary T cells from cord blood	blood
29	chr1:84944400-84944600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr1:84944400-84944600	Active TSS	Primary hematopoietic stem cells	blood
31	chr1:84944400-84944600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:84944400-84944600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:84944400-84944600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:84944400-84944600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:84944400-84944600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr1:84944400-84944600	Bivalent Enhancer	Fetal Intestine Large	intestine
37	chr1:84944400-84944600	Bivalent/Poised TSS	Fetal Kidney	kidney
38	chr1:84944400-84944600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
39	chr1:84944400-84944600	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr1:84944400-84944600	Flanking Active TSS	Right Atrium	heart
41	chr1:84944400-84944600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:84944400-84944600	Flanking Bivalent TSS/Enh	Thymus	Thymus
43	chr1:84944400-84944800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:84944400-84944800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:84944400-84944800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:84944400-84944800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
47	chr1:84944400-84944800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:84944400-84944800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:84944400-84944800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr1:84944400-84944800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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