Variant report

Variant	rs536594060
Chromosome Location	chr3:49591113-49591114
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	RCOR1	chr3:49590843-49591398	K562	blood:	n/a	n/a
2	CEBPB	chr3:49590627-49591233	A549	lung:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
3	CEBPB	chr3:49590681-49591121	MCF-7	breast:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
4	CEBPB	chr3:49590774-49591120	A549	lung:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
5	REST	chr3:49590593-49593431	HL-60	blood:	n/a	chr3:49591201-49591211 chr3:49590761-49590779 chr3:49592639-49592653 chr3:49590764-49590777 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
6	CEBPB	chr3:49590673-49591186	ECC-1	luminal epithelium:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
7	CEBPB	chr3:49590732-49591137	Hela-S3	cervix:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
8	CEBPB	chr3:49590721-49591119	K562	blood:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
9	BHLHE40	chr3:49591017-49591659	K562	blood:	n/a	n/a
10	POLR2A	chr3:49591070-49591980	H1-hESC	embryonic stem cell:	n/a	n/a
11	BRCA1	chr3:49590858-49591122	Hela-S3	cervix:	n/a	n/a
12	JUND	chr3:49591004-49591204	H1-hESC	embryonic stem cell:	n/a	chr3:49591144-49591156
13	REST	chr3:49590783-49593080	H1-neurons	neurons:	n/a	chr3:49591201-49591211 chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
14	FOS	chr3:49590827-49591137	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr3:49590741-49591116	A549	lung:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
16	CEBPB	chr3:49590716-49591152	ECC-1	luminal epithelium:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
17	SIN3A	chr3:49591074-49592777	H1-hESC	embryonic stem cell:	n/a	chr3:49592638-49592652 chr3:49591201-49591210
18	JUN	chr3:49590843-49591164	HepG2	liver:	n/a	chr3:49591000-49591013 chr3:49591144-49591156
19	KAP1	chr3:49590902-49591725	HEK293	kidney:	n/a	n/a
20	GATA3	chr3:49590999-49591260	SH-SY5Y	brain:	n/a	n/a
21	CEBPB	chr3:49590694-49591147	K562	blood:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
22	RCOR1	chr3:49590681-49592523	IMR90	lung:	n/a	n/a
23	CEBPB	chr3:49590737-49591186	MCF-7	breast:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
24	CEBPB	chr3:49590746-49591119	HepG2	liver:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
25	JUND	chr3:49590823-49591223	HepG2	liver:	n/a	chr3:49591144-49591156
26	POLR2A	chr3:49591027-49591132	IMR90	lung:	n/a	n/a
27	CEBPB	chr3:49590748-49591122	H1-hESC	embryonic stem cell:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
28	CEBPB	chr3:49590737-49591129	IMR90	lung:	n/a	chr3:49590925-49590934 chr3:49590923-49590934
29	SETDB1	chr3:49590817-49591746	U2OS	brain:	n/a	n/a
30	MAX	chr3:49591059-49592752	HepG2	liver:	n/a	chr3:49591131-49591141

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49590547..49592695-chr3:49709214..49711684,3	MCF-7	breast:
2	chr3:49582614..49585275-chr3:49588937..49591341,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NICN1-1	chr3:49590981-49591120	ENSG00000226913
2	lnc-NICN1-1	chr3:49590981-49591120	XLOC_003118
3	lnc-NICN1-1	chr3:49590374-49591536	NONHSAT089709

Variant related genes	Relation type
BSN	TF binding region
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3325224	chr3:49590473-49593321	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49589000-49591200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49589400-49591200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr3:49589600-49591200	Enhancers	Primary hematopoietic stem cells	blood
4	chr3:49590400-49591200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:49590400-49591400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49590400-49591400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr3:49590600-49591200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:49590600-49591200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:49590600-49591200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49590600-49591200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr3:49590600-49591200	Enhancers	Esophagus	oesophagus
12	chr3:49590600-49591200	Enhancers	Fetal Intestine Small	intestine
13	chr3:49590600-49591200	Enhancers	Fetal Muscle Trunk	muscle
14	chr3:49590600-49591200	Enhancers	Placenta	Placenta
15	chr3:49590600-49591200	Enhancers	Hela-S3	cervix
16	chr3:49590600-49591200	Flanking Active TSS	HepG2	liver
17	chr3:49590600-49591400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:49590600-49591400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:49590600-49591400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:49590600-49591400	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr3:49590600-49591400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr3:49590600-49591600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr3:49590600-49591600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:49590600-49591600	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr3:49590600-49591600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr3:49590600-49591600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:49590600-49591800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr3:49590600-49591800	Flanking Active TSS	Dnd41	blood
29	chr3:49590800-49591200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:49590800-49591200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:49590800-49591200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr3:49590800-49591200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:49590800-49591200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:49590800-49591200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:49590800-49591200	Enhancers	Fetal Intestine Large	intestine
36	chr3:49590800-49591200	Enhancers	GM12878-XiMat	blood
37	chr3:49590800-49591400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:49590800-49591400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:49590800-49591400	Enhancers	Fetal Heart	heart
40	chr3:49590800-49591400	Enhancers	Spleen	Spleen
41	chr3:49590800-49591600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:49590800-49591600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:49590800-49591600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49590800-49591600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:49590800-49591600	Flanking Active TSS	Liver	Liver
46	chr3:49590800-49591600	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr3:49590800-49591600	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr3:49590800-49591600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:49590800-49591600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr3:49590800-49591800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood

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