Variant report

Variant	rs538980513
Chromosome Location	chr3:51988425-51988426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:51988404-51988455	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr3:51988245-51988540	NB4	blood:	n/a	n/a
3	POLR2A	chr3:51988208-51988456	MCF10A-Er-Src	breast:	n/a	n/a
4	SPI1	chr3:51987421-51988653	HL-60	blood:	n/a	n/a
5	SPI1	chr3:51988146-51988431	GM12891	blood:	n/a	n/a
6	SPI1	chr3:51988232-51988451	GM12891	blood:	n/a	n/a
7	SPI1	chr3:51988203-51988451	K562	blood:	n/a	n/a
8	SPI1	chr3:51988070-51988565	HL-60	blood:	n/a	n/a
9	POLR2A	chr3:51987786-51988483	HepG2	liver:	n/a	n/a
10	MAX	chr3:51988278-51988511	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:51988425-51988475	HPAEpiC	pulmonary alveolar:	n/a
2	chr3:51988425-51988475	U87	brain:	n/a
3	chr3:51988425-51988475	Hepatocyte	liver:	n/a
4	chr3:51988425-51988475	HCPEpiC	choroid plexus:	n/a
5	chr3:51988425-51988475	AG09319	gingival:	n/a
6	chr3:51988425-51988475	HEEpiC	esophagus:	n/a
7	chr3:51988425-51988475	ECC-1	luminal epithelium:	n/a
8	chr3:51988425-51988475	MCF10A-Er-Src	breast:	n/a
9	chr3:51988425-51988475	HNPCEpiC	eye:	n/a
10	chr3:51988425-51988475	Hela-S3	cervix:	n/a
11	chr3:51988425-51988475	HIPEpiC	eye:	n/a
12	chr3:51988425-51988475	Caco-2	colon:	n/a
13	chr3:51988425-51988475	HEK293	kidney:	embryo
14	chr3:51988425-51988475	ProgFib	skin:	n/a
15	chr3:51988425-51988475	BE2_C	brain:	n/a
16	chr3:51988425-51988475	GM06990	blood:	n/a
17	chr3:51988425-51988475	CMK	blood:	n/a
18	chr3:51988425-51988475	NHDF-neo	bronchial:	n/a
19	chr3:51988425-51988475	RPTEC	kidney:	n/a
20	chr3:51988425-51988475	MCF-7	breast:	n/a
21	chr3:51988425-51988475	SAEC	small airway:	n/a
22	chr3:51988425-51988475	T-47D	breast:	n/a
23	chr3:51988425-51988475	PANC-1	pancreas:	n/a
24	chr3:51988425-51988475	AG09309	skin:	n/a
25	chr3:51988425-51988475	HMEC	breast:	n/a
26	chr3:51988425-51988475	SKMC	muscle:	n/a
27	chr3:51988425-51988475	AG10803	skin:	n/a
28	chr3:51988425-51988475	GM12878	blood:	n/a
29	chr3:51988425-51988475	Jurkat	blood:	n/a
30	chr3:51988425-51988475	IMR90	lung:	fetal
31	chr3:51988425-51988475	PFSK-1	brain:	n/a
32	chr3:51988425-51988475	AG04449	skin:	fetal
33	chr3:51988425-51988475	HRPEpiC	eye:	n/a
34	chr3:51988425-51988475	AG04450	lung:	fetal
35	chr3:51988425-51988475	NHBE	bronchial:	n/a
36	chr3:51988425-51988475	HCF	heart:	n/a
37	chr3:51988425-51988475	HAEpiC	amniotic membrane:	n/a
38	chr3:51988425-51988475	HUVEC	blood vessel:	n/a
39	chr3:51988425-51988475	H1-hESC	embryonic stem cell:	embryo
40	chr3:51988425-51988475	GM12892	blood:	n/a
41	chr3:51988425-51988475	HRCEpiC	kidney:	n/a
42	chr3:51988425-51988475	SK-N-SH_RA	brain:	n/a
43	chr3:51988425-51988475	HepG2	liver:	n/a
44	chr3:51988425-51988475	GM19239	blood:	n/a
45	chr3:51988425-51988475	AoSMC	blood vessel:	n/a
46	chr3:51988425-51988475	HL-60	blood:	n/a
47	chr3:51988425-51988475	NB4	blood:	n/a
48	chr3:51988425-51988475	GM12891	blood:	n/a
49	chr3:51988425-51988475	LNCaP	prostate:	n/a
50	chr3:51988425-51988475	NT2-D1	testis:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51980605..51983550-chr3:51988202..51990542,2	MCF-7	breast:
2	chr3:51987928..51991924-chr3:52001407..52003695,4	MCF-7	breast:
3	chr3:51988009..51992311-chr3:51992660..51997455,6	K562	blood:
4	chr3:51987614..51990073-chr3:52025987..52029912,3	K562	blood:
5	chr3:51985305..51989166-chr3:51989564..51992012,3	K562	blood:

No data

Variant related genes	Relation type
GPR62	TF binding region
GPR62	CpG island
ENSG00000090097	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	esv3438711	chr3:51987612-51992410	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51977200-51989200	Weak transcription	Ovary	ovary
2	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
3	chr3:51977400-51989200	Weak transcription	Esophagus	oesophagus
4	chr3:51977600-51989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:51977600-51989000	Weak transcription	Pancreas	Pancrea
6	chr3:51977600-51989400	Weak transcription	Left Ventricle	heart
7	chr3:51977800-51989400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:51980400-51989400	Weak transcription	Right Ventricle	heart
9	chr3:51980600-51989200	Weak transcription	Gastric	stomach
10	chr3:51983400-51989000	Weak transcription	Brain Anterior Caudate	brain
11	chr3:51983400-51989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:51983400-51989000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:51983400-51989400	Weak transcription	Lung	lung
14	chr3:51983600-51989000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:51983600-51989200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:51983600-51989200	Weak transcription	Adipose Nuclei	Adipose
17	chr3:51983600-51989200	Weak transcription	Spleen	Spleen
18	chr3:51983800-51990200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:51984000-51989200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:51984400-51989200	Weak transcription	Liver	Liver
21	chr3:51986200-51993400	Weak transcription	HepG2	liver
22	chr3:51987000-51989000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:51987200-51989000	Enhancers	Brain Angular Gyrus	brain
24	chr3:51987200-51989000	Enhancers	Brain Hippocampus Middle	brain
25	chr3:51987400-51988800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:51987600-51989400	Enhancers	Brain Substantia Nigra	brain
27	chr3:51987600-51990200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
28	chr3:51987600-51992000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:51987800-51989000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr3:51987800-51989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:51987800-51989200	Weak transcription	Psoas Muscle	Psoas
32	chr3:51988000-51989000	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:51988000-51989400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:51988000-51989600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:51988000-51990600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:51988000-51990800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:51988000-51990800	Weak transcription	HSMM	muscle
38	chr3:51988000-51992400	Weak transcription	HSMMtube	muscle
39	chr3:51988200-51989400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:51988200-51989400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:51988200-51989400	Weak transcription	Right Atrium	heart
42	chr3:51988200-51989600	Weak transcription	Osteobl	bone
43	chr3:51988400-51988600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
44	chr3:51988400-51988600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:51988400-51989000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:51988400-52000600	Weak transcription	Hela-S3	cervix

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