Variant report

Variant	rs7652753
Chromosome Location	chr3:100118978-100118979
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:100118920-100121749	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:100118927-100121609	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:100118252-100121519	K562	blood:	n/a	n/a
4	MAZ	chr3:100118953-100121748	IMR90	lung:	n/a	chr3:100120332-100120342
5	HCFC1	chr3:100118890-100122089	Hela-S3	cervix:	n/a	n/a
6	SIN3A	chr3:100118787-100121306	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr3:100118433-100122085	IMR90	lung:	n/a	n/a
8	MXI1	chr3:100118461-100122114	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:100118940-100120898	HUVEC	blood vessel:	n/a	n/a
10	WRNIP1	chr3:100118812-100119579	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:100118877-100121951	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:100118213-100122018	HepG2	liver:	n/a	n/a
13	SIN3AK20	chr3:100118847-100120979	MCF-7	breast:	n/a	n/a
14	POLR2A	chr3:100118885-100119597	GM12878	blood:	n/a	n/a
15	MXI1	chr3:100118905-100120707	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:100118960-100119010	HEK293	kidney:	embryo
2	chr3:100118960-100119010	A549	lung:	n/a
3	chr3:100118960-100119010	AoSMC	blood vessel:	n/a
4	chr3:100118960-100119010	SKMC	muscle:	n/a
5	chr3:100118960-100119010	GM06990	blood:	n/a
6	chr3:100118960-100119010	ovcar-3	ovarian:	n/a
7	chr3:100118960-100119010	MCF10A-Er-Src	breast:	n/a
8	chr3:100118960-100119010	HepG2	liver:	n/a
9	chr3:100118960-100119010	HCT-116	colon:	n/a
10	chr3:100118960-100119010	HUVEC	blood vessel:	n/a
11	chr3:100118960-100119010	AG04450	lung:	fetal
12	chr3:100118960-100119010	SAEC	small airway:	n/a
13	chr3:100118960-100119010	SK-N-SH	brain:	n/a
14	chr3:100118960-100119010	NHBE	bronchial:	n/a
15	chr3:100118960-100119010	NT2-D1	testis:	n/a
16	chr3:100118960-100119010	Jurkat	blood:	n/a
17	chr3:100118960-100119010	Caco-2	colon:	n/a
18	chr3:100118960-100119010	MCF-7	breast:	n/a
19	chr3:100118960-100119010	HRCEpiC	kidney:	n/a
20	chr3:100118960-100119010	GM12891	blood:	n/a
21	chr3:100118960-100119010	NHDF-neo	bronchial:	n/a
22	chr3:100118960-100119010	U87	brain:	n/a
23	chr3:100118960-100119010	PANC-1	pancreas:	n/a
24	chr3:100118960-100119010	Hepatocyte	liver:	n/a
25	chr3:100118960-100119010	HRPEpiC	eye:	n/a
26	chr3:100118960-100119010	HMEC	breast:	n/a
27	chr3:100118960-100119010	AG10803	skin:	n/a
28	chr3:100118960-100119010	HCF	heart:	n/a
29	chr3:100118960-100119010	LNCaP	prostate:	n/a
30	chr3:100118960-100119010	NB4	blood:	n/a
31	chr3:100118960-100119010	HAEpiC	amniotic membrane:	n/a
32	chr3:100118960-100119010	GM12892	blood:	n/a
33	chr3:100118960-100119010	AG09319	gingival:	n/a
34	chr3:100118960-100119010	IMR90	lung:	fetal
35	chr3:100118960-100119010	RPTEC	kidney:	n/a
36	chr3:100118960-100119010	HRE	kidney:	n/a
37	chr3:100118960-100119010	GM19239	blood:	n/a
38	chr3:100118960-100119010	ECC-1	luminal epithelium:	n/a
39	chr3:100118960-100119010	K562	blood:	n/a
40	chr3:100118960-100119010	HCM	heart:	n/a
41	chr3:100118960-100119010	GM12878	blood:	n/a
42	chr3:100118960-100119010	SK-N-SH_RA	brain:	n/a
43	chr3:100118960-100119010	HNPCEpiC	eye:	n/a
44	chr3:100118960-100119010	H1-hESC	embryonic stem cell:	embryo
45	chr3:100118960-100119010	BE2_C	brain:	n/a
46	chr3:100118960-100119010	AG04449	skin:	fetal
47	chr3:100118960-100119010	PrEC	prostate:	n/a
48	chr3:100118960-100119010	HIPEpiC	eye:	n/a
49	chr3:100118960-100119010	ProgFib	skin:	n/a
50	chr3:100118960-100119010	NH-A	brain:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:
2	chr3:100117960..100119967-chr3:100122961..100124652,2	K562	blood:
3	chr3:100118702..100121299-chr3:100427057..100432444,4	K562	blood:
4	chr3:99541055..99543601-chr3:100118284..100119899,2	K562	blood:
5	chr3:100106736..100109063-chr3:100117268..100119845,2	K562	blood:
6	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
7	chr3:100118496..100120943-chr3:101229402..101232050,2	K562	blood:
8	chr3:99979418..99981870-chr3:100118340..100121144,2	K562	blood:
9	chr3:100093392..100095134-chr3:100117257..100119612,2	K562	blood:
10	chr3:100116980..100119109-chr3:100147635..100150466,2	K562	blood:
11	chr3:99996650..99998446-chr3:100117737..100119944,2	K562	blood:
12	chr3:100099401..100103527-chr3:100117550..100121361,6	MCF-7	breast:
13	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:

No data

Variant related genes	Relation type
LNP1	TF binding region
LNP1	CpG island
ENSG00000036054	Chromatin interaction
ENSG00000114354	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000138468	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16842137	1.00[AMR][1000 genomes]
rs403858	1.00[AMR][1000 genomes]
rs55978866	1.00[AMR][1000 genomes]
rs56678433	1.00[AMR][1000 genomes]
rs58283662	1.00[AMR][1000 genomes]
rs58869093	1.00[AMR][1000 genomes]
rs62636639	1.00[AMR][1000 genomes]
rs6441136	1.00[AMR][1000 genomes]
rs6441243	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6788019	1.00[AMR][1000 genomes]
rs6788854	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6788875	1.00[AMR][1000 genomes]
rs73862419	1.00[AMR][1000 genomes]
rs73862437	1.00[AMR][1000 genomes]
rs73862440	1.00[AMR][1000 genomes]
rs73862445	1.00[AMR][1000 genomes]
rs73862453	1.00[AMR][1000 genomes]
rs7630901	1.00[AMR][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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 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	chr3:100116800-100121600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:100117000-100119000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:100117000-100123000	Active TSS	K562	blood
4	chr3:100117400-100119000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:100117600-100119600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr3:100117600-100121000	Active TSS	Fetal Kidney	kidney
7	chr3:100117800-100119000	Active TSS	Rectal Smooth Muscle	rectum
8	chr3:100117800-100119000	Flanking Active TSS	Dnd41	blood
9	chr3:100117800-100119200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:100117800-100119200	Flanking Active TSS	Liver	Liver
11	chr3:100117800-100119400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:100117800-100119400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr3:100117800-100122800	Active TSS	Right Atrium	heart
14	chr3:100118000-100119000	Flanking Active TSS	Psoas Muscle	Psoas
15	chr3:100118000-100119400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:100118200-100119000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:100118200-100119000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr3:100118200-100119000	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:100118200-100119000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:100118200-100119000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:100118200-100119000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:100118200-100119000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:100118200-100119000	Flanking Active TSS	Fetal Brain Female	brain
24	chr3:100118200-100119000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:100118200-100119000	Flanking Active TSS	Hela-S3	cervix
26	chr3:100118200-100119000	Flanking Active TSS	NHEK	skin
27	chr3:100118200-100119200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:100118200-100119200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:100118200-100119200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:100118200-100119200	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr3:100118200-100119200	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr3:100118200-100119200	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr3:100118200-100119200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:100118200-100119200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr3:100118200-100119200	Flanking Active TSS	Fetal Brain Male	brain
36	chr3:100118200-100119200	Flanking Active TSS	Fetal Thymus	thymus
37	chr3:100118200-100119200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:100118200-100119200	Flanking Active TSS	HUVEC	blood vessel
39	chr3:100118200-100119200	Flanking Active TSS	Osteobl	bone
40	chr3:100118200-100119400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr3:100118200-100119400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:100118200-100119400	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr3:100118200-100119400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:100118200-100119400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr3:100118200-100119600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:100118200-100119800	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr3:100118200-100120000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:100118200-100122000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:100118200-100122000	Active TSS	Left Ventricle	heart
50	chr3:100118200-100122400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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