Variant report

Variant	rs561905975
Chromosome Location	chr3:49591551-49591552
allele	C/T
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	POLR2A	chr3:49591524-49592002	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr3:49591226-49592017	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:49591487-49592088	ECC-1	luminal epithelium:	n/a	n/a
4	MTA3	chr3:49591180-49591705	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49591186-49592081	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr3:49591355-49591974	ECC-1	luminal epithelium:	n/a	chr3:49591403-49591413 chr3:49591404-49591411
7	POLR2A	chr3:49591535-49591841	U87	brain:	n/a	n/a
8	MAX	chr3:49591293-49592008	A549	lung:	n/a	n/a
9	MAZ	chr3:49591551-49591954	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:49591470-49591948	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49591410-49592072	H1-neurons	neurons:	n/a	n/a
12	E2F6	chr3:49591515-49592003	A549	lung:	n/a	chr3:49591894-49591903 chr3:49591940-49591950
13	POLR2A	chr3:49591506-49592083	HEK293	kidney:	n/a	n/a
14	POLR2A	chr3:49591485-49592045	K562	blood:	n/a	n/a
15	CEBPB	chr3:49591532-49591725	H1-hESC	embryonic stem cell:	n/a	n/a
16	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
17	REST	chr3:49591469-49592776	U87	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
18	PAX5	chr3:49591524-49591870	GM12878	blood:	n/a	chr3:49591800-49591809
19	CREB1	chr3:49591316-49592050	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr3:49591481-49592787	GM12878	blood:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
21	TBP	chr3:49591432-49591920	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:49591505-49592058	MCF-7	breast:	n/a	n/a
23	RCOR1	chr3:49591526-49592427	HepG2	liver:	n/a	n/a
24	MAZ	chr3:49591231-49592453	IMR90	lung:	n/a	n/a
25	MYBL2	chr3:49591366-49591782	HepG2	liver:	n/a	n/a
26	NRF1	chr3:49591400-49592220	SK-N-SH	brain:	n/a	chr3:49591802-49591811 chr3:49591893-49591902 chr3:49591893-49591907 chr3:49591893-49591904 chr3:49591890-49591904 chr3:49591911-49591922 chr3:49591895-49591904 chr3:49591893-49591904
27	POLR2A	chr3:49591541-49591911	K562	blood:	n/a	n/a
28	REST	chr3:49591520-49592852	PFSK-1	brain:	n/a	chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
29	POLR2A	chr3:49591114-49592109	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:49591460-49591985	ECC-1	luminal epithelium:	n/a	n/a
31	MAX	chr3:49591123-49592666	HepG2	liver:	n/a	chr3:49591131-49591141
32	REST	chr3:49591543-49592638	U87	brain:	n/a	n/a
33	BHLHE40	chr3:49591017-49591659	K562	blood:	n/a	n/a
34	POLR2A	chr3:49591070-49591980	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:49591482-49592026	K562	blood:	n/a	n/a
36	HEY1	chr3:49591459-49592054	HepG2	liver:	n/a	chr3:49591915-49591930 chr3:49591943-49591958 chr3:49591940-49591955
37	MAX	chr3:49591409-49592453	K562	blood:	n/a	n/a
38	CREB1	chr3:49591348-49591976	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:49591466-49591928	MCF-7	breast:	n/a	n/a
40	POLR2A	chr3:49591533-49591729	HepG2	liver:	n/a	n/a
41	SIN3AK20	chr3:49591551-49591916	HepG2	liver:	n/a	n/a
42	MAZ	chr3:49591538-49591985	GM12878	blood:	n/a	n/a
43	YY1	chr3:49591534-49592359	K562	blood:	n/a	chr3:49591911-49591925 chr3:49591905-49591916 chr3:49591802-49591816 chr3:49591908-49591922 chr3:49591943-49591954 chr3:49591939-49591953 chr3:49591951-49591960 chr3:49591945-49591959 chr3:49591935-49591943 chr3:49591911-49591920 chr3:49591922-49591944 chr3:49591905-49591919
44	JUND	chr3:49591538-49591904	K562	blood:	n/a	n/a
45	PAX5	chr3:49591531-49592420	GM12892	blood:	n/a	chr3:49591800-49591809
46	TAF1	chr3:49591396-49592256	ECC-1	luminal epithelium:	n/a	n/a
47	REST	chr3:49590783-49593080	H1-neurons	neurons:	n/a	chr3:49591201-49591211 chr3:49592639-49592653 chr3:49592634-49592652 chr3:49592633-49592653 chr3:49592633-49592653
48	POLR2A	chr3:49591542-49591801	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:49591336-49592113	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr3:49591550-49591907	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49590547..49592695-chr3:49709214..49711684,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NICN1-1	chr3:49591474-49591799	ENSG00000226913
2	lnc-NICN1-1	chr3:49591474-49591773	ENSG00000226913
3	lnc-NICN1-1	chr3:49591526-49591610	XLOC_003118
4	lnc-NICN1-1	chr3:49591526-49591732	NONHSAT089707

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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49590600-49591600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
2	chr3:49590600-49591600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:49590600-49591600	Flanking Active TSS	Brain Angular Gyrus	brain
4	chr3:49590600-49591600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:49590600-49591600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:49590600-49591800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr3:49590600-49591800	Flanking Active TSS	Dnd41	blood
8	chr3:49590800-49591600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:49590800-49591600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:49590800-49591600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:49590800-49591600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:49590800-49591600	Flanking Active TSS	Liver	Liver
13	chr3:49590800-49591600	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr3:49590800-49591600	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr3:49590800-49591600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:49590800-49591600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr3:49590800-49591800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
18	chr3:49590800-49592400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr3:49591000-49591600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:49591000-49591600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:49591000-49591600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:49591000-49591600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:49591000-49591600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
24	chr3:49591000-49591600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:49591000-49591600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr3:49591000-49591600	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr3:49591000-49591600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr3:49591000-49591600	Flanking Active TSS	Fetal Brain Male	brain
29	chr3:49591000-49591600	Flanking Active TSS	Fetal Lung	lung
30	chr3:49591000-49591600	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr3:49591000-49591600	Flanking Active TSS	Fetal Stomach	stomach
32	chr3:49591000-49591600	Flanking Active TSS	Lung	lung
33	chr3:49591000-49591600	Flanking Active TSS	Osteobl	bone
34	chr3:49591000-49591800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr3:49591000-49591800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:49591000-49591800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:49591000-49591800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:49591000-49591800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr3:49591000-49591800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
40	chr3:49591000-49591800	Flanking Active TSS	HUVEC	blood vessel
41	chr3:49591000-49591800	Flanking Active TSS	NHEK	skin
42	chr3:49591000-49592200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr3:49591000-49592400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr3:49591000-49592400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:49591000-49592800	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:49591200-49591600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:49591200-49591600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr3:49591200-49591600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr3:49591200-49591600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:49591200-49591600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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