Variant report

Variant	rs577938802
Chromosome Location	chr2:99552996-99552997
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	CTCF	chr2:99552905-99553001	Lung_OC	lung:	n/a	n/a
2	CTCF	chr2:99552980-99553130	HRE	kidney:	n/a	n/a
3	RAD21	chr2:99552857-99553115	SK-N-SH_RA	brain:	n/a	chr2:99552994-99553006
4	CTCF	chr2:99552940-99553090	GM12873	blood:	n/a	n/a
5	POLR2A	chr2:99552373-99553176	MCF-7	breast:	n/a	n/a
6	CTCF	chr2:99552900-99553050	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr2:99552960-99553110	HRPEpiC	eye:	n/a	n/a
8	RAD21	chr2:99552911-99553063	SK-N-SH_RA	brain:	n/a	chr2:99552994-99553006
9	CTCF	chr2:99552960-99553110	GM12864	blood:	n/a	n/a
10	CTCF	chr2:99552920-99553070	HBMEC	blood vessel:	n/a	n/a
11	CTCF	chr2:99552870-99553048	GM12892	blood:	n/a	n/a
12	RAD21	chr2:99552753-99553192	ECC-1	luminal epithelium:	n/a	chr2:99552994-99553006
13	CTCF	chr2:99552940-99553090	AG04449	skin:	n/a	n/a
14	CTCF	chr2:99552880-99553030	HMF	breast:	n/a	n/a
15	CTCF	chr2:99552860-99553010	HepG2	liver:	n/a	n/a
16	CTCF	chr2:99552883-99553014	NHEK	skin:	n/a	n/a
17	CTCF	chr2:99552846-99553040	LNCaP	prostate:	n/a	n/a
18	CTCF	chr2:99552900-99553050	MCF-7	breast:	n/a	n/a
19	CTCF	chr2:99552880-99553030	HEK293	kidney:	n/a	n/a
20	CTCF	chr2:99552897-99553013	MCF-7	breast:	n/a	n/a
21	CTCF	chr2:99552860-99553010	HEK293	kidney:	n/a	n/a
22	CTCF	chr2:99552931-99553028	GM19240	blood:	n/a	n/a
23	CTCF	chr2:99552820-99553045	A549	lung:	n/a	n/a
24	CTCF	chr2:99552880-99553030	WERI-Rb-1	eye:	n/a	n/a
25	SPI1	chr2:99552954-99553211	GM12891	blood:	n/a	n/a
26	CTCF	chr2:99552940-99553090	SAEC	small airway:	n/a	n/a
27	CTCF	chr2:99552880-99553030	A549	lung:	n/a	n/a
28	CTCF	chr2:99552880-99553030	HRPEpiC	eye:	n/a	n/a
29	ZBTB7A	chr2:99552076-99553329	ECC-1	luminal epithelium:	n/a	chr2:99552914-99552923
30	RAD21	chr2:99552838-99553085	H1-hESC	embryonic stem cell:	n/a	chr2:99552994-99553006
31	CTCF	chr2:99552860-99553010	NB4	blood:	n/a	n/a
32	CTCF	chr2:99552880-99553030	GM12873	blood:	n/a	n/a
33	CTCF	chr2:99552870-99553066	A549	lung:	n/a	n/a
34	CTCF	chr2:99552872-99553056	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr2:99552860-99553010	GM12869	blood:	n/a	n/a
36	CTCF	chr2:99552900-99553050	HMEC	breast:	n/a	n/a
37	CTCF	chr2:99552882-99553041	Gliobla	brain:	n/a	n/a
38	CTCF	chr2:99552920-99553070	GM12870	blood:	n/a	n/a
39	RAD21	chr2:99552794-99553115	HepG2	liver:	n/a	chr2:99552994-99553006
40	CTCF	chr2:99552942-99553034	GM13977	blood:	n/a	n/a
41	CTCF	chr2:99552860-99553010	GM12866	blood:	n/a	n/a
42	CTCF	chr2:99552880-99553030	RPTEC	kidney:	n/a	n/a
43	CTCF	chr2:99552960-99553110	GM12875	blood:	n/a	n/a
44	CTCF	chr2:99552763-99553145	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr2:99552484-99553169	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr2:99552903-99553035	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr2:99552900-99553050	GM12868	blood:	n/a	n/a
48	CTCF	chr2:99552907-99552997	Fibrobl	skin:	n/a	n/a
49	CTCF	chr2:99552880-99553030	GM12871	blood:	n/a	n/a
50	CTCF	chr2:99552900-99553050	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
KIAA1211L	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv834310	chr2:99533832-99709999	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3339215	chr2:99550420-99554818	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3412425	chr2:99551545-99553993	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99549400-99553800	Active TSS	Brain Anterior Caudate	brain
2	chr2:99550000-99553800	Active TSS	Brain Angular Gyrus	brain
3	chr2:99550800-99553200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr2:99551200-99553800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:99551200-99554000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:99551400-99553800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
7	chr2:99551800-99553000	Bivalent/Poised TSS	HUVEC	blood vessel
8	chr2:99551800-99553200	Active TSS	Ovary	ovary
9	chr2:99551800-99553600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:99551800-99553600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:99551800-99553800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr2:99551800-99553800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:99551800-99554000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:99551800-99554000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:99552000-99553000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:99552000-99553000	Active TSS	Aorta	Aorta
17	chr2:99552000-99553000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
18	chr2:99552000-99553000	Bivalent/Poised TSS	HSMMtube	muscle
19	chr2:99552000-99553200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
20	chr2:99552000-99553200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr2:99552000-99553200	Bivalent/Poised TSS	Osteobl	bone
22	chr2:99552000-99553400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr2:99552000-99553600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:99552000-99553600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:99552000-99553600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:99552000-99553600	Bivalent/Poised TSS	Psoas Muscle	Psoas
27	chr2:99552000-99553600	Active TSS	Right Atrium	heart
28	chr2:99552000-99553800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:99552000-99553800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr2:99552000-99553800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:99552000-99553800	Active TSS	Gastric	stomach
32	chr2:99552200-99553000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:99552200-99553000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:99552200-99553000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr2:99552200-99553000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr2:99552200-99553000	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr2:99552200-99553000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:99552200-99553000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:99552200-99553000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr2:99552200-99553000	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr2:99552200-99553000	Active TSS	Pancreas	Pancrea
42	chr2:99552200-99553000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:99552200-99553000	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr2:99552200-99553000	Bivalent/Poised TSS	Stomach Mucosa	stomach
45	chr2:99552200-99553000	Active TSS	Stomach Smooth Muscle	stomach
46	chr2:99552200-99553000	Bivalent/Poised TSS	HepG2	liver
47	chr2:99552200-99553200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:99552200-99553200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:99552200-99553200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr2:99552200-99553200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links