Variant report

Variant	rs72773678
Chromosome Location	chr5:98105558-98105559
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	MAX	chr5:98105071-98105764	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr5:98103774-98105621	GM12878	blood:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
3	ZNF143	chr5:98104707-98105688	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr5:98105016-98105848	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr5:98103702-98106617	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr5:98105540-98105690	MCF-7	breast:	n/a	n/a
7	CEBPB	chr5:98103920-98105849	IMR90	lung:	n/a	n/a
8	MAZ	chr5:98105529-98105695	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:98104495-98105818	H1-neurons	neurons:	n/a	n/a
10	SIN3A	chr5:98103375-98106650	H1-hESC	embryonic stem cell:	n/a	chr5:98103604-98103613
11	TBP	chr5:98104562-98106316	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr5:98105420-98105570	HMF	breast:	n/a	n/a
13	TCF7L2	chr5:98104758-98106785	HCT-116	colon:	n/a	n/a
14	CTCF	chr5:98105500-98105650	GM12868	blood:	n/a	n/a
15	RCOR1	chr5:98103712-98107759	IMR90	lung:	n/a	n/a
16	SIN3AK20	chr5:98104719-98106946	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr5:98105500-98105650	NHEK	skin:	n/a	n/a
18	SMC3	chr5:98103216-98107662	SK-N-SH	brain:	n/a	chr5:98104937-98104947 chr5:98104933-98104947
19	CTCF	chr5:98105480-98105630	Caco-2	colon:	n/a	n/a
20	SIN3AK20	chr5:98105469-98105754	PANC-1	pancreas:	n/a	n/a
21	MAZ	chr5:98103628-98107877	IMR90	lung:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
22	NANOG	chr5:98105400-98105747	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:98105261-98107576	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr5:98105500-98105650	GM12869	blood:	n/a	n/a
25	CTBP2	chr5:98103882-98106770	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr5:98105540-98105690	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr5:98105480-98105630	HMEC	breast:	n/a	n/a
28	TAF1	chr5:98104550-98105689	H1-neurons	neurons:	n/a	n/a
29	CTCF	chr5:98105500-98105650	AG04450	lung:	n/a	n/a
30	CTCF	chr5:98105480-98105630	GM12869	blood:	n/a	n/a
31	ZNF263	chr5:98103812-98107566	HEK293-T-REx	kidney:	n/a	chr5:98104029-98104038
32	MYC	chr5:98105445-98105643	MCF10A-Er-Src	breast:	n/a	n/a
33	TCF12	chr5:98104738-98105621	SK-N-SH	brain:	n/a	n/a
34	MAX	chr5:98104732-98105775	SK-N-SH	brain:	n/a	chr5:98104887-98104896
35	FOXA2	chr5:98104998-98105699	A549	lung:	n/a	n/a
36	CTCF	chr5:98105420-98105570	GM12873	blood:	n/a	n/a
37	CTCF	chr5:98105480-98105630	GM12870	blood:	n/a	n/a
38	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
39	POLR2A	chr5:98104331-98107644	U87	brain:	n/a	n/a
40	CTCF	chr5:98105500-98105650	GM12873	blood:	n/a	n/a
41	POLR2A	chr5:98104882-98105639	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr5:98104325-98107650	U87	brain:	n/a	n/a
43	CTCF	chr5:98105420-98105570	BJ	skin:	n/a	n/a
44	CTCF	chr5:98105420-98105570	GM12874	blood:	n/a	n/a
45	CTCF	chr5:98105420-98105570	SAEC	small airway:	n/a	n/a
46	CTCF	chr5:98105540-98105690	GM12874	blood:	n/a	n/a
47	POLR2A	chr5:98105369-98105730	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr5:98103207-98107631	IMR90	lung:	n/a	chr5:98104757-98104769 chr5:98104608-98104620 chr5:98104932-98104951 chr5:98104937-98104949 chr5:98104937-98104947
49	PBX3	chr5:98104784-98105585	SK-N-SH	brain:	n/a	n/a
50	RAD21	chr5:98103065-98107819	SK-N-SH	brain:	n/a	chr5:98104757-98104769 chr5:98104608-98104620 chr5:98104932-98104951 chr5:98104937-98104949 chr5:98104937-98104947

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
2	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1-1	chr5:98105322-98106888	ENSG00000246763.2
2	lnc-CHD1-1	chr5:98105322-98106888	ENSG00000246763.2
3	lnc-CHD1-1	chr5:98105322-98106888	NR_033932
4	lnc-CHD1-1	chr5:98105229-98105957	NONHSAT102949
5	lnc-CHD1-1	chr5:98105229-98105957	NONHSAT102950

Variant related genes	Relation type
RGMB	TF binding region
ENSG00000246763	Chromatin interaction
ENSG00000174136	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10463991	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10463992	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10900866	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11242488	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12513899	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12515608	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12518567	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12521450	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17166353	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2080892	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271218	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302981	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302983	0.84[ASN][1000 genomes]
rs3952931	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4018049	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59968659	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67111144	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67755922	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68077609	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6888898	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773643	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773645	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773646	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72773650	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773652	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773654	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72773674	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72773675	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7727348	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[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	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98103200-98107200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:98103400-98107400	Active TSS	Aorta	Aorta
3	chr5:98103400-98107600	Active TSS	Brain Anterior Caudate	brain
4	chr5:98103800-98105600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr5:98103800-98106200	Active TSS	Fetal Brain Female	brain
6	chr5:98103800-98107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:98103800-98107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr5:98103800-98107400	Flanking Active TSS	Liver	Liver
9	chr5:98103800-98107400	Active TSS	Brain Angular Gyrus	brain
10	chr5:98103800-98107400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:98103800-98107400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr5:98103800-98107600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr5:98103800-98107800	Active TSS	Brain Cingulate Gyrus	brain
14	chr5:98103800-98108000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:98103800-98108000	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr5:98103800-98108200	Active TSS	Fetal Kidney	kidney
17	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
18	chr5:98104000-98105600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:98104000-98106400	Active TSS	NHDF-Ad	bronchial
20	chr5:98104000-98106600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr5:98104000-98106600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:98104000-98106600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr5:98104000-98107000	Active TSS	Stomach Mucosa	stomach
24	chr5:98104000-98107200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:98104000-98107200	Active TSS	Gastric	stomach
26	chr5:98104000-98107400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
28	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
29	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:98104000-98107400	Active TSS	Brain Substantia Nigra	brain
31	chr5:98104000-98107400	Active TSS	Left Ventricle	heart
32	chr5:98104000-98107400	Active TSS	Ovary	ovary
33	chr5:98104000-98107400	Active TSS	Pancreas	Pancrea
34	chr5:98104000-98107600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr5:98104000-98107600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
37	chr5:98104000-98107600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr5:98104000-98107800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:98104000-98108200	Active TSS	Fetal Intestine Large	intestine
41	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
42	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:98104200-98105600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:98104200-98105800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:98104200-98106000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:98104200-98106000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr5:98104200-98107400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:98104200-98108000	Active TSS	Brain Hippocampus Middle	brain
49	chr5:98104200-98111600	Active TSS	Right Atrium	heart
50	chr5:98104400-98105600	Flanking Active TSS	Colonic Mucosa	Colon

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