Variant report

Variant	rs58631862
Chromosome Location	chr5:98106245-98106246
allele	A/C
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	NFIC	chr5:98106090-98106814	ECC-1	luminal epithelium:	n/a	n/a
2	TCF7L2	chr5:98105601-98106821	Hela-S3	cervix:	n/a	n/a
3	ATF3	chr5:98106243-98106521	K562	blood:	n/a	n/a
4	TCF12	chr5:98103702-98106617	SK-N-SH	brain:	n/a	n/a
5	CEBPB	chr5:98106089-98107566	IMR90	lung:	n/a	chr5:98106944-98106961
6	RCOR1	chr5:98106022-98107574	Hela-S3	cervix:	n/a	n/a
7	SIN3A	chr5:98103375-98106650	H1-hESC	embryonic stem cell:	n/a	chr5:98103604-98103613
8	TBP	chr5:98104562-98106316	H1-hESC	embryonic stem cell:	n/a	n/a
9	ELK1	chr5:98105890-98106299	Hela-S3	cervix:	n/a	n/a
10	CHD2	chr5:98106231-98106669	Hela-S3	cervix:	n/a	n/a
11	TCF7L2	chr5:98104758-98106785	HCT-116	colon:	n/a	n/a
12	RCOR1	chr5:98103712-98107759	IMR90	lung:	n/a	n/a
13	SIN3AK20	chr5:98104719-98106946	SK-N-SH	brain:	n/a	n/a
14	TAF1	chr5:98106165-98106622	SK-N-SH	brain:	n/a	n/a
15	SMC3	chr5:98103216-98107662	SK-N-SH	brain:	n/a	chr5:98104937-98104947 chr5:98104933-98104947
16	MAZ	chr5:98103628-98107877	IMR90	lung:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
17	POLR2A	chr5:98105261-98107576	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr5:98105814-98106600	HUVEC	blood vessel:	n/a	n/a
19	ATF2	chr5:98105994-98106824	GM12878	blood:	n/a	n/a
20	CTBP2	chr5:98103882-98106770	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF143	chr5:98106165-98106446	Hela-S3	cervix:	n/a	n/a
22	MAX	chr5:98105591-98106774	A549	lung:	n/a	n/a
23	TAF1	chr5:98105961-98106389	H1-hESC	embryonic stem cell:	n/a	n/a
24	RFX5	chr5:98106172-98107639	Hela-S3	cervix:	n/a	n/a
25	NFIC	chr5:98105876-98106850	ECC-1	luminal epithelium:	n/a	n/a
26	CEBPB	chr5:98106226-98106545	K562	blood:	n/a	n/a
27	SMC3	chr5:98106003-98107608	Hela-S3	cervix:	n/a	n/a
28	ZNF263	chr5:98103812-98107566	HEK293-T-REx	kidney:	n/a	chr5:98104029-98104038
29	GTF2F1	chr5:98106028-98107561	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr5:98106087-98107006	A549	lung:	n/a	chr5:98106944-98106961
31	HDAC2	chr5:98105971-98106526	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
33	POLR2A	chr5:98104331-98107644	U87	brain:	n/a	n/a
34	CEBPB	chr5:98106048-98106998	A549	lung:	n/a	chr5:98106944-98106961
35	STAT1	chr5:98106002-98106288	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:98104325-98107650	U87	brain:	n/a	n/a
37	CTCF	chr5:98106180-98106330	HepG2	liver:	n/a	n/a
38	TBL1XR1	chr5:98105996-98106618	GM12878	blood:	n/a	n/a
39	RAD21	chr5:98103207-98107631	IMR90	lung:	n/a	chr5:98104757-98104769 chr5:98104608-98104620 chr5:98104932-98104951 chr5:98104937-98104949 chr5:98104937-98104947
40	CHD2	chr5:98105850-98106423	H1-hESC	embryonic stem cell:	n/a	n/a
41	CEBPB	chr5:98105860-98107619	Hela-S3	cervix:	n/a	chr5:98106944-98106961
42	TCF7L2	chr5:98105924-98106528	PANC-1	pancreas:	n/a	n/a
43	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
44	CTCF	chr5:98106140-98106290	GM12874	blood:	n/a	n/a
45	JUND	chr5:98106196-98106472	K562	blood:	n/a	n/a
46	CTCF	chr5:98106100-98106250	GM12870	blood:	n/a	n/a
47	CTCF	chr5:98103564-98106247	A549	lung:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
48	ATF2	chr5:98106077-98106662	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr5:98105942-98106590	H1-neurons	neurons:	n/a	n/a
50	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648

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

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

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10515282	0.81[AMR][1000 genomes]
rs12653617	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17166344	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56926200	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	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:127 , 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	chr5:98103800-98107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:98103800-98107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr5:98103800-98107400	Flanking Active TSS	Liver	Liver
7	chr5:98103800-98107400	Active TSS	Brain Angular Gyrus	brain
8	chr5:98103800-98107400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:98103800-98107400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:98103800-98107600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr5:98103800-98107800	Active TSS	Brain Cingulate Gyrus	brain
12	chr5:98103800-98108000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:98103800-98108000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:98103800-98108200	Active TSS	Fetal Kidney	kidney
15	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
16	chr5:98104000-98106400	Active TSS	NHDF-Ad	bronchial
17	chr5:98104000-98106600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr5:98104000-98106600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:98104000-98106600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr5:98104000-98107000	Active TSS	Stomach Mucosa	stomach
21	chr5:98104000-98107200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:98104000-98107200	Active TSS	Gastric	stomach
23	chr5:98104000-98107400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
25	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
26	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:98104000-98107400	Active TSS	Brain Substantia Nigra	brain
28	chr5:98104000-98107400	Active TSS	Left Ventricle	heart
29	chr5:98104000-98107400	Active TSS	Ovary	ovary
30	chr5:98104000-98107400	Active TSS	Pancreas	Pancrea
31	chr5:98104000-98107600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
32	chr5:98104000-98107600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr5:98104000-98107600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr5:98104000-98107800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:98104000-98108200	Active TSS	Fetal Intestine Large	intestine
38	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
39	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:98104200-98107400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:98104200-98108000	Active TSS	Brain Hippocampus Middle	brain
42	chr5:98104200-98111600	Active TSS	Right Atrium	heart
43	chr5:98104400-98106400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:98104400-98106600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr5:98104400-98107000	Active TSS	Small Intestine	intestine
46	chr5:98104400-98107400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:98104400-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
48	chr5:98104400-98107400	Active TSS	Osteobl	bone
49	chr5:98104400-98107600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:98104400-98107800	Active TSS	NHLF	lung

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