Variant report

Variant	rs62156558
Chromosome Location	chr2:99553104-99553105
allele	G/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	CTCF	chr2:99552980-99553130	HRE	kidney:	n/a	n/a
2	RAD21	chr2:99552857-99553115	SK-N-SH_RA	brain:	n/a	chr2:99552994-99553006
3	POLR2A	chr2:99552373-99553176	MCF-7	breast:	n/a	n/a
4	CTCF	chr2:99552960-99553110	HRPEpiC	eye:	n/a	n/a
5	CTCF	chr2:99552960-99553110	GM12864	blood:	n/a	n/a
6	RAD21	chr2:99552753-99553192	ECC-1	luminal epithelium:	n/a	chr2:99552994-99553006
7	CTCF	chr2:99553060-99553210	HMEC	breast:	n/a	n/a
8	POLR2A	chr2:99553027-99553247	MCF10A-Er-Src	breast:	n/a	n/a
9	SIN3A	chr2:99553064-99553943	H1-hESC	embryonic stem cell:	n/a	n/a
10	SPI1	chr2:99552954-99553211	GM12891	blood:	n/a	n/a
11	ZBTB7A	chr2:99552076-99553329	ECC-1	luminal epithelium:	n/a	chr2:99552914-99552923
12	BACH1	chr2:99553086-99554164	H1-hESC	embryonic stem cell:	n/a	chr2:99554105-99554119
13	FOS	chr2:99553103-99553333	MCF10A-Er-Src	breast:	n/a	chr2:99553204-99553215
14	RAD21	chr2:99552794-99553115	HepG2	liver:	n/a	chr2:99552994-99553006
15	CTCF	chr2:99552960-99553110	GM12875	blood:	n/a	n/a
16	CTCF	chr2:99552763-99553145	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:99552484-99553169	ECC-1	luminal epithelium:	n/a	n/a
18	EGR1	chr2:99552499-99553441	HCT-116	colon:	n/a	chr2:99552768-99552781 chr2:99552769-99552779 chr2:99552769-99552780 chr2:99552820-99552829 chr2:99552693-99552707 chr2:99553406-99553415 chr2:99553128-99553141
19	EGR1	chr2:99552504-99553416	HCT-116	colon:	n/a	chr2:99552768-99552781 chr2:99552769-99552779 chr2:99552769-99552780 chr2:99552820-99552829 chr2:99552693-99552707 chr2:99553406-99553415 chr2:99553128-99553141
20	HDAC2	chr2:99552336-99553107	MCF-7	breast:	n/a	n/a
21	CTCF	chr2:99553100-99553250	MCF-7	breast:	n/a	n/a
22	ZNF143	chr2:99552944-99553138	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr2:99552763-99553136	H1-hESC	embryonic stem cell:	n/a	n/a
24	EGR1	chr2:99552920-99553382	MCF-7	breast:	n/a	chr2:99553128-99553141
25	POU2F2	chr2:99553072-99553317	GM12891	blood:	n/a	chr2:99553155-99553170 chr2:99553159-99553167 chr2:99553153-99553174
26	CTCF	chr2:99553020-99553170	HCT-116	colon:	n/a	n/a
27	RAD21	chr2:99552441-99553229	H1-hESC	embryonic stem cell:	n/a	chr2:99552651-99552665 chr2:99552994-99553006
28	ZBTB7A	chr2:99552710-99553343	ECC-1	luminal epithelium:	n/a	chr2:99552914-99552923
29	RAD21	chr2:99552820-99553172	H1-hESC	embryonic stem cell:	n/a	chr2:99552994-99553006

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:99553078-99553128	BJ	skin:	n/a
2	chr2:99553078-99553128	HEEpiC	esophagus:	n/a
3	chr2:99553055-99553105	HCT-116	colon:	n/a
4	chr2:99553078-99553128	NT2-D1	testis:	n/a
5	chr2:99553078-99553128	GM12878	blood:	n/a
6	chr2:99553055-99553105	HCPEpiC	choroid plexus:	n/a
7	chr2:99553055-99553105	HAEpiC	amniotic membrane:	n/a
8	chr2:99553055-99553105	Jurkat	blood:	n/a
9	chr2:99553078-99553128	K562	blood:	n/a
10	chr2:99553055-99553105	SK-N-MC	brain:	n/a
11	chr2:99553078-99553128	GM19239	blood:	n/a
12	chr2:99553078-99553128	ProgFib	skin:	n/a
13	chr2:99553078-99553128	T-47D	breast:	n/a
14	chr2:99553055-99553105	AG09309	skin:	n/a
15	chr2:99553055-99553105	GM19239	blood:	n/a
16	chr2:99553078-99553128	MCF10A-Er-Src	breast:	n/a
17	chr2:99553078-99553128	HPAEpiC	pulmonary alveolar:	n/a
18	chr2:99553078-99553128	AG10803	skin:	n/a
19	chr2:99553078-99553128	SK-N-MC	brain:	n/a
20	chr2:99553078-99553128	PANC-1	pancreas:	n/a
21	chr2:99553078-99553128	SAEC	small airway:	n/a
22	chr2:99553055-99553105	A549	lung:	n/a
23	chr2:99553078-99553128	CMK	blood:	n/a
24	chr2:99553078-99553128	HCPEpiC	choroid plexus:	n/a
25	chr2:99553055-99553105	HPAEpiC	pulmonary alveolar:	n/a
26	chr2:99553055-99553105	HIPEpiC	eye:	n/a
27	chr2:99553055-99553105	SAEC	small airway:	n/a
28	chr2:99553055-99553105	LNCaP	prostate:	n/a
29	chr2:99553078-99553128	HUVEC	blood vessel:	n/a
30	chr2:99553078-99553128	HIPEpiC	eye:	n/a
31	chr2:99553055-99553105	RPTEC	kidney:	n/a
32	chr2:99553055-99553105	NHBE	bronchial:	n/a
33	chr2:99553078-99553128	BE2_C	brain:	n/a
34	chr2:99553055-99553105	SK-N-SH_RA	brain:	n/a
35	chr2:99553078-99553128	A549	lung:	n/a
36	chr2:99553078-99553128	SK-N-SH_RA	brain:	n/a
37	chr2:99553055-99553105	HCM	heart:	n/a
38	chr2:99553055-99553105	HNPCEpiC	eye:	n/a
39	chr2:99553055-99553105	NB4	blood:	n/a
40	chr2:99553078-99553128	MCF-7	breast:	n/a
41	chr2:99553055-99553105	HL-60	blood:	n/a
42	chr2:99553055-99553105	Caco-2	colon:	n/a
43	chr2:99553055-99553105	PrEC	prostate:	n/a
44	chr2:99553078-99553128	Jurkat	blood:	n/a
45	chr2:99553055-99553105	HRCEpiC	kidney:	n/a
46	chr2:99553078-99553128	HL-60	blood:	n/a
47	chr2:99553055-99553105	AG10803	skin:	n/a
48	chr2:99553055-99553105	MCF-7	breast:	n/a
49	chr2:99553078-99553128	AG04450	lung:	fetal
50	chr2:99553078-99553128	U87	brain:	n/a

Variant related genes	Relation type
KIAA1211L	TF binding region
KIAA1211L	CpG island

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10165534	0.81[EUR][1000 genomes]
rs10181422	0.85[AMR][1000 genomes]
rs10196680	0.81[EUR][1000 genomes]
rs10202452	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12464710	0.81[EUR][1000 genomes]
rs12467679	0.80[EUR][1000 genomes]
rs12477754	0.81[EUR][1000 genomes]
rs13396358	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13407840	0.85[AMR][1000 genomes]
rs13412764	0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1349778	0.81[EUR][1000 genomes]
rs1453564	0.85[AMR][1000 genomes]
rs1530996	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1580068	0.81[EUR][1000 genomes]
rs28575117	0.83[AMR][1000 genomes]
rs35001733	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4585080	0.86[AMR][1000 genomes]
rs4622780	0.81[EUR][1000 genomes]
rs4851179	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4851183	0.81[AMR][1000 genomes]
rs6542846	0.85[AMR][1000 genomes]
rs6542852	0.82[EUR][1000 genomes]
rs6704766	0.81[EUR][1000 genomes]
rs6721535	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6722164	0.85[AMR][1000 genomes]
rs6724476	0.81[AMR][1000 genomes]
rs6732579	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6740035	0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6740054	0.83[AMR][1000 genomes]
rs6740267	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6759354	0.81[EUR][1000 genomes]
rs7558239	0.81[EUR][1000 genomes]
rs7571390	0.83[AMR][1000 genomes]
rs7586608	0.85[AMR][1000 genomes]
rs7591794	0.85[AMR][1000 genomes]
rs9308816	0.81[EUR][1000 genomes]
rs9808541	0.81[EUR][1000 genomes]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62156558	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs62156558	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs62156558	TSGA10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

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	chr2:99551800-99553200	Active TSS	Ovary	ovary
8	chr2:99551800-99553600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:99551800-99553600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:99551800-99553800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:99551800-99553800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:99551800-99554000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:99551800-99554000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:99552000-99553200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
15	chr2:99552000-99553200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
16	chr2:99552000-99553200	Bivalent/Poised TSS	Osteobl	bone
17	chr2:99552000-99553400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr2:99552000-99553600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:99552000-99553600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:99552000-99553600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:99552000-99553600	Bivalent/Poised TSS	Psoas Muscle	Psoas
22	chr2:99552000-99553600	Active TSS	Right Atrium	heart
23	chr2:99552000-99553800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:99552000-99553800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr2:99552000-99553800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:99552000-99553800	Active TSS	Gastric	stomach
27	chr2:99552200-99553200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:99552200-99553200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:99552200-99553200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr2:99552200-99553200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:99552200-99553200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:99552200-99553200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:99552200-99553200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
34	chr2:99552200-99553200	Bivalent/Poised TSS	Fetal Brain Female	brain
35	chr2:99552200-99553200	Active TSS	HMEC	breast
36	chr2:99552200-99553400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr2:99552200-99553400	Active TSS	Esophagus	oesophagus
38	chr2:99552200-99553400	Active TSS	A549	lung
39	chr2:99552200-99553400	Bivalent/Poised TSS	NHEK	skin
40	chr2:99552200-99553600	Bivalent/Poised TSS	HSMM	muscle
41	chr2:99552200-99553800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
42	chr2:99552200-99553800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr2:99552200-99554000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr2:99552200-99554000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
45	chr2:99552200-99554000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr2:99552400-99553200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr2:99552400-99553600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:99552400-99553800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:99552400-99553800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr2:99552600-99553600	Enhancers	Liver	Liver

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