Variant report

Variant	rs562965556
Chromosome Location	chr2:46925439-46925440
allele	-/AGG
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	chr2:46925418-46926670	HUVEC	blood vessel:	n/a	n/a
2	MAZ	chr2:46925281-46926947	K562	blood:	n/a	chr2:46925915-46925924 chr2:46925914-46925925 chr2:46926001-46926010 chr2:46925914-46925923 chr2:46925913-46925926 chr2:46925913-46925926 chr2:46925571-46925581 chr2:46925914-46925925 chr2:46926003-46926012 chr2:46925915-46925924 chr2:46925915-46925924 chr2:46926002-46926013
3	FOSL2	chr2:46924693-46926291	HepG2	liver:	n/a	chr2:46925640-46925647 chr2:46925638-46925647
4	SIX5	chr2:46925262-46926233	A549	lung:	n/a	n/a
5	POLR2A	chr2:46925418-46926823	MCF-7	breast:	n/a	n/a
6	TEAD4	chr2:46924885-46926138	HepG2	liver:	n/a	n/a
7	JUND	chr2:46925385-46926988	GM12878	blood:	n/a	chr2:46925637-46925648 chr2:46925640-46925647 chr2:46925638-46925647 chr2:46926567-46926576
8	BRCA1	chr2:46925405-46926193	Hela-S3	cervix:	n/a	n/a
9	PBX3	chr2:46925306-46926690	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr2:46925429-46926220	PANC-1	pancreas:	n/a	n/a
11	YY1	chr2:46925349-46926348	ECC-1	luminal epithelium:	n/a	chr2:46925661-46925670 chr2:46926086-46926096 chr2:46926085-46926093 chr2:46926074-46926096
12	POLR2A	chr2:46925377-46926318	H1-neurons	neurons:	n/a	n/a
13	MAZ	chr2:46924871-46926829	HepG2	liver:	n/a	chr2:46925915-46925924 chr2:46925914-46925925 chr2:46926001-46926010 chr2:46925914-46925923 chr2:46925913-46925926 chr2:46925913-46925926 chr2:46925571-46925581 chr2:46925914-46925925 chr2:46926003-46926012 chr2:46925915-46925924 chr2:46925915-46925924 chr2:46926002-46926013
14	POLR2A	chr2:46925388-46926186	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:46925358-46926841	Hela-S3	cervix:	n/a	n/a
16	REST	chr2:46925359-46926253	HL-60	blood:	n/a	n/a
17	HEY1	chr2:46925386-46926266	K562	blood:	n/a	n/a
18	POLR2A	chr2:46925398-46926843	MCF10A-Er-Src	breast:	n/a	n/a
19	MTA3	chr2:46925288-46926123	GM12878	blood:	n/a	n/a
20	ELF1	chr2:46925341-46926347	MCF-7	breast:	n/a	n/a
21	SP1	chr2:46925418-46926444	H1-hESC	embryonic stem cell:	n/a	chr2:46925660-46925672 chr2:46925657-46925671 chr2:46925662-46925671 chr2:46926212-46926224 chr2:46925988-46925997 chr2:46925958-46925969 chr2:46926158-46926172 chr2:46926186-46926207 chr2:46925661-46925670 chr2:46925662-46925671
22	EP300	chr2:46925388-46926323	A549	lung:	n/a	chr2:46926092-46926108 chr2:46925638-46925647
23	YY1	chr2:46925396-46926299	K562	blood:	n/a	chr2:46925661-46925670 chr2:46926086-46926096 chr2:46926085-46926093 chr2:46926074-46926096
24	TEAD4	chr2:46925328-46926422	SK-N-SH	brain:	n/a	n/a
25	PML	chr2:46925386-46926228	GM12878	blood:	n/a	chr2:46925640-46925649
26	FOSL1	chr2:46925386-46925845	K562	blood:	n/a	chr2:46925640-46925647 chr2:46925638-46925647
27	SIN3AK20	chr2:46925261-46926363	MCF-7	breast:	n/a	n/a
28	NFIC	chr2:46925407-46926173	GM12878	blood:	n/a	n/a
29	FOSL2	chr2:46925242-46926310	SK-N-SH	brain:	n/a	chr2:46925640-46925647 chr2:46925638-46925647
30	POLR2A	chr2:46925376-46926800	K562	blood:	n/a	n/a
31	SMARCB1	chr2:46925067-46927153	Hela-S3	cervix:	n/a	n/a
32	USF2	chr2:46925261-46926210	Hela-S3	cervix:	n/a	chr2:46926002-46926013
33	FOSL2	chr2:46925438-46926077	MCF-7	breast:	n/a	chr2:46925640-46925647 chr2:46925638-46925647
34	TCF12	chr2:46925027-46926468	A549	lung:	n/a	n/a
35	POLR2A	chr2:46925388-46926250	PANC-1	pancreas:	n/a	n/a
36	MYC	chr2:46925180-46927073	A549	lung:	n/a	chr2:46925915-46925924 chr2:46925914-46925925 chr2:46926001-46926010 chr2:46925914-46925923 chr2:46925913-46925926 chr2:46925913-46925926 chr2:46925571-46925581 chr2:46925914-46925925 chr2:46926003-46926012 chr2:46925915-46925924 chr2:46925915-46925924 chr2:46926002-46926013
37	MAX	chr2:46925409-46927060	ECC-1	luminal epithelium:	n/a	chr2:46925915-46925924 chr2:46925914-46925925 chr2:46926001-46926010 chr2:46925914-46925923 chr2:46925913-46925926 chr2:46925913-46925926 chr2:46925571-46925581 chr2:46925914-46925925 chr2:46926003-46926012 chr2:46925915-46925924 chr2:46925915-46925924 chr2:46926002-46926013
38	POLR2A	chr2:46925420-46926248	Hela-S3	cervix:	n/a	n/a
39	MXI1	chr2:46925267-46927660	IMR90	lung:	n/a	chr2:46926004-46926013 chr2:46926023-46926032
40	POLR2A	chr2:46925292-46926598	U87	brain:	n/a	n/a
41	POLR2A	chr2:46925386-46926240	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr2:46925320-46926903	GM18505	blood:	n/a	n/a
43	FOS	chr2:46925430-46926100	HUVEC	blood vessel:	n/a	chr2:46925640-46925647 chr2:46925638-46925647 chr2:46925637-46925648
44	MAX	chr2:46925436-46926297	HCT-116	colon:	n/a	chr2:46925915-46925924 chr2:46925914-46925925 chr2:46926001-46926010 chr2:46925914-46925923 chr2:46925913-46925926 chr2:46925913-46925926 chr2:46925571-46925581 chr2:46925914-46925925 chr2:46926003-46926012 chr2:46925915-46925924 chr2:46925915-46925924 chr2:46926002-46926013
45	SP4	chr2:46925413-46926227	H1-hESC	embryonic stem cell:	n/a	chr2:46925658-46925674 chr2:46925958-46925969
46	MXI1	chr2:46924630-46927097	HepG2	liver:	n/a	chr2:46926004-46926013 chr2:46926023-46926032
47	YY1	chr2:46925425-46926267	H1-hESC	embryonic stem cell:	n/a	chr2:46925661-46925670 chr2:46926086-46926096 chr2:46926085-46926093 chr2:46926074-46926096
48	CBX3	chr2:46925392-46926259	K562	blood:	n/a	n/a
49	YY1	chr2:46925312-46926471	SK-N-SH	brain:	n/a	chr2:46925661-46925670 chr2:46926086-46926096 chr2:46926085-46926093 chr2:46926074-46926096
50	USF1	chr2:46925432-46926333	ECC-1	luminal epithelium:	n/a	chr2:46925914-46925925

No.	Distal block	Cell Line	Cell type
1	chr2:46897133..46898995-chr2:46922668..46925477,2	K562	blood:
2	chr2:46923183..46926073-chr2:46944483..46946206,2	K562	blood:
3	chr2:46842180..46843861-chr2:46924432..46926384,2	K562	blood:
4	chr2:46923714..46925684-chr2:46963885..46966277,2	MCF-7	breast:
5	chr2:46919753..46923455-chr2:46923473..46925760,5	K562	blood:
6	chr2:46916264..46918533-chr2:46923065..46926019,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGF-4	chr2:46925253-46925831	NONHSAT070524

Variant related genes	Relation type
SOCS5	TF binding region
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv3365634	chr2:46910377-46929000	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3460455	chr2:46910422-46928955	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3460454	chr2:46910435-46928955	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3460456	chr2:46910436-46928951	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv3343605	chr2:46925273-46927821	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46924600-46929200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:46924800-46925600	Enhancers	Gastric	stomach
3	chr2:46924800-46925600	Enhancers	Lung	lung
4	chr2:46924800-46925600	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr2:46924800-46925800	Flanking Active TSS	Dnd41	blood
6	chr2:46924800-46928200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr2:46925000-46925600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:46925000-46925600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr2:46925000-46925600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr2:46925000-46925600	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr2:46925000-46925600	Flanking Active TSS	Colonic Mucosa	Colon
12	chr2:46925000-46925600	Enhancers	Fetal Brain Male	brain
13	chr2:46925000-46925600	Enhancers	Stomach Mucosa	stomach
14	chr2:46925000-46925600	Flanking Active TSS	A549	lung
15	chr2:46925000-46925600	Flanking Active TSS	Hela-S3	cervix
16	chr2:46925000-46925600	Enhancers	NHDF-Ad	bronchial
17	chr2:46925000-46925800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:46925000-46925800	Weak transcription	Small Intestine	intestine
19	chr2:46925000-46926000	Flanking Active TSS	K562	blood
20	chr2:46925000-46927200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:46925000-46927200	Active TSS	Duodenum Mucosa	Duodenum
22	chr2:46925000-46928400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:46925000-46930000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr2:46925200-46925600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:46925200-46925600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:46925200-46925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:46925200-46925600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr2:46925200-46925600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr2:46925200-46925600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:46925200-46925600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:46925200-46925600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:46925200-46925600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr2:46925200-46925600	Flanking Active TSS	Liver	Liver
34	chr2:46925200-46925600	Flanking Active TSS	Fetal Heart	heart
35	chr2:46925200-46925600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr2:46925200-46925600	Flanking Active TSS	Fetal Stomach	stomach
37	chr2:46925200-46925600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:46925200-46925600	Flanking Active TSS	Thymus	Thymus
39	chr2:46925200-46925800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr2:46925200-46925800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr2:46925200-46925800	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr2:46925200-46925800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr2:46925200-46925800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr2:46925200-46925800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr2:46925200-46925800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr2:46925200-46925800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:46925200-46925800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:46925200-46925800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr2:46925200-46925800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:46925200-46925800	Flanking Active TSS	Fetal Muscle Trunk	muscle

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