Variant report

Variant	rs1110002
Chromosome Location	chr2:171572292-171572293
allele	C/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	POLR2A	chr2:171571679-171574265	HepG2	liver:	n/a	n/a
2	BACH1	chr2:171572121-171572528	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr2:171572260-171572377	GM19240	blood:	n/a	n/a
4	HNF4A	chr2:171570620-171573709	HepG2	liver:	n/a	chr2:171572142-171572160 chr2:171572143-171572158
5	HNF4G	chr2:171570905-171572522	HepG2	liver:	n/a	chr2:171572142-171572160 chr2:171572143-171572158
6	MAX	chr2:171571756-171572340	H1-hESC	embryonic stem cell:	n/a	chr2:171572090-171572100
7	MAX	chr2:171570793-171572577	HCT-116	colon:	n/a	chr2:171572484-171572494 chr2:171572090-171572100
8	CTCF	chr2:171572280-171572430	AG04449	skin:	n/a	n/a
9	MAX	chr2:171571580-171572531	A549	lung:	n/a	chr2:171572484-171572494 chr2:171572090-171572100
10	CEBPD	chr2:171570697-171573739	HepG2	liver:	n/a	n/a
11	MYBL2	chr2:171570699-171572565	HepG2	liver:	n/a	n/a
12	E2F6	chr2:171571778-171572351	A549	lung:	n/a	chr2:171572092-171572104
13	NFIC	chr2:171570759-171572599	HepG2	liver:	n/a	n/a
14	MAX	chr2:171567494-171574371	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
15	MAX	chr2:171571665-171572498	H1-hESC	embryonic stem cell:	n/a	chr2:171572484-171572494 chr2:171572090-171572100
16	CHD2	chr2:171569669-171572660	HepG2	liver:	n/a	n/a
17	CBX3	chr2:171570404-171572616	K562	blood:	n/a	n/a
18	CTCF	chr2:171572247-171572384	GM19238	blood:	n/a	n/a
19	MXI1	chr2:171570562-171574086	HepG2	liver:	n/a	n/a
20	NFIC	chr2:171570706-171572595	ECC-1	luminal epithelium:	n/a	n/a
21	CTCF	chr2:171572240-171572390	NHLF	lung:	n/a	n/a
22	MAX	chr2:171571617-171572725	ECC-1	luminal epithelium:	n/a	chr2:171572484-171572494 chr2:171572090-171572100
23	TCF7L2	chr2:171571064-171572330	MCF-7	breast:	n/a	chr2:171571733-171571749 chr2:171571540-171571556 chr2:171571543-171571552 chr2:171571758-171571772 chr2:171571734-171571748 chr2:171571759-171571773 chr2:171571540-171571556 chr2:171571761-171571770 chr2:171571734-171571748 chr2:171571699-171571706 chr2:171571733-171571749
24	ZNF263	chr2:171571532-171572626	HEK293-T-REx	kidney:	n/a	chr2:171572354-171572363
25	POLR2A	chr2:171571720-171573222	HepG2	liver:	n/a	n/a
26	MAX	chr2:171567137-171574353	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
27	E2F6	chr2:171570655-171572360	K562	blood:	n/a	chr2:171571753-171571761 chr2:171571487-171571499 chr2:171571605-171571620 chr2:171571606-171571620 chr2:171571362-171571372 chr2:171572092-171572104
28	POLR2A	chr2:171571577-171574339	HepG2	liver:	n/a	n/a
29	TCF7L2	chr2:171571079-171572320	HepG2	liver:	n/a	chr2:171571733-171571749 chr2:171571540-171571556 chr2:171571543-171571552 chr2:171571758-171571772 chr2:171571734-171571748 chr2:171571759-171571773 chr2:171571540-171571556 chr2:171571761-171571770 chr2:171571734-171571748 chr2:171571699-171571706 chr2:171571733-171571749
30	TAF1	chr2:171571636-171574190	HepG2	liver:	n/a	n/a
31	SETDB1	chr2:171571737-171572503	K562	blood:	n/a	n/a
32	CTCF	chr2:171572277-171572369	Pancreas_OC	pancreas:	n/a	n/a
33	YY1	chr2:171571681-171574134	HepG2	liver:	n/a	chr2:171571931-171571945 chr2:171574026-171574038 chr2:171571977-171571986
34	HEY1	chr2:171566552-171576261	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
35	E2F6	chr2:171571160-171572533	A549	lung:	n/a	chr2:171571753-171571761 chr2:171571487-171571499 chr2:171571605-171571620 chr2:171572415-171572424 chr2:171571606-171571620 chr2:171571362-171571372 chr2:171572092-171572104
36	TAF1	chr2:171571706-171573224	HepG2	liver:	n/a	n/a
37	E2F6	chr2:171571693-171572466	H1-hESC	embryonic stem cell:	n/a	chr2:171571753-171571761 chr2:171572415-171572424 chr2:171572092-171572104
38	YY1	chr2:171571623-171572337	H1-hESC	embryonic stem cell:	n/a	chr2:171571931-171571945 chr2:171571977-171571986
39	TBP	chr2:171570730-171572906	HepG2	liver:	n/a	n/a
40	MAX	chr2:171571732-171572338	A549	lung:	n/a	chr2:171572090-171572100
41	MYC	chr2:171571932-171572349	MCF-7	breast:	n/a	chr2:171572090-171572100
42	HNF4A	chr2:171570937-171572512	HepG2	liver:	n/a	chr2:171572142-171572160 chr2:171572143-171572158
43	HEY1	chr2:171566435-171575595	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
44	NFIC	chr2:171571426-171572553	ECC-1	luminal epithelium:	n/a	n/a
45	EP300	chr2:171570756-171572480	HepG2	liver:	n/a	chr2:171571903-171571919 chr2:171572408-171572424 chr2:171571976-171571985
46	CTCF	chr2:171572187-171572481	GM12878	blood:	n/a	n/a
47	CTBP2	chr2:171571428-171572498	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr2:171570742-171572545	HepG2	liver:	n/a	chr2:171572305-171572318
49	MAX	chr2:171571689-171572666	ECC-1	luminal epithelium:	n/a	chr2:171572484-171572494 chr2:171572090-171572100
50	CTCF	chr2:171572220-171572370	Caco-2	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:171571171..171574868-chr2:171624858..171628652,5	K562	blood:
2	chr2:171568787..171573894-chr2:171626202..171629385,10	K562	blood:
3	chr2:171570330..171572699-chr2:171627295..171629894,2	MCF-7	breast:
4	chr2:171571182..171573160-chr2:171784797..171786624,2	K562	blood:

Variant related genes	Relation type
LINC01124	TF binding region
SP5	TF binding region
ENSG00000115806	Chromatin interaction
ENSG00000239467	Chromatin interaction
ENSG00000234350	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1065651	0.84[AMR][1000 genomes]
rs1134626	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12463871	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12469431	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472397	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1362488	0.84[AMR][1000 genomes]
rs1420378	0.82[AMR][1000 genomes]
rs1420379	0.82[AMR][1000 genomes]
rs1420380	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1420381	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17694562	0.84[AMR][1000 genomes]
rs17694708	0.85[AMR][1000 genomes]
rs17751035	0.84[AMR][1000 genomes]
rs17751072	0.84[AMR][1000 genomes]
rs17751234	0.84[AMR][1000 genomes]
rs1861464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990653	0.84[AMR][1000 genomes]
rs2356234	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34436957	0.82[AMR][1000 genomes]
rs35127716	0.89[AMR][1000 genomes]
rs35872782	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4667657	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668308	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668315	0.84[AMR][1000 genomes]
rs55693618	0.85[AMR][1000 genomes]
rs55799517	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55804482	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55923006	0.85[AMR][1000 genomes]
rs56024406	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56330225	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56364811	0.85[AMR][1000 genomes]
rs58919807	0.82[AMR][1000 genomes]
rs61246559	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62168365	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62168366	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62168367	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62168369	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168370	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168371	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62168373	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62168376	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62168396	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62168397	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62168399	0.84[AMR][1000 genomes]
rs62168400	0.84[AMR][1000 genomes]
rs62168401	0.84[AMR][1000 genomes]
rs62168446	0.89[AMR][1000 genomes]
rs62168448	0.89[AMR][1000 genomes]
rs62169546	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62169547	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62169548	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6712113	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742220	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72885464	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72885487	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72887356	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72887361	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72887372	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7600585	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875409	chr2:171565376-171577859	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv821786	chr2:171567780-171574707	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv583609	chr2:171568633-171573309	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583610	chr2:171568633-171573529	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15608	chr2:171569890-171574062	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171569200-171573000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr2:171569400-171574400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:171569600-171574800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:171569600-171575600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:171569800-171572400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:171569800-171572600	Flanking Active TSS	Liver	Liver
7	chr2:171570000-171572600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:171570000-171572600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
9	chr2:171570000-171572600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
10	chr2:171570000-171572600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
11	chr2:171570000-171573200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:171570000-171574000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr2:171570000-171575600	Bivalent/Poised TSS	HepG2	liver
14	chr2:171570000-171576200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:171570200-171572400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:171570200-171572600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:171570200-171573800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr2:171570200-171574200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:171570200-171574400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr2:171570200-171576200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:171570400-171572400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
22	chr2:171570400-171572600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr2:171570400-171572600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
24	chr2:171570400-171572600	Flanking Bivalent TSS/Enh	HMEC	breast
25	chr2:171570400-171573000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr2:171570400-171573400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr2:171570400-171574000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:171570400-171574200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:171570400-171576200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:171570600-171572400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
31	chr2:171570600-171572600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
32	chr2:171570600-171572600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr2:171570600-171572600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr2:171570600-171573000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
35	chr2:171570600-171573400	Active TSS	Aorta	Aorta
36	chr2:171570600-171574000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
37	chr2:171570800-171572400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:171570800-171572400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
39	chr2:171570800-171572400	Active TSS	Gastric	stomach
40	chr2:171570800-171572400	Bivalent/Poised TSS	A549	lung
41	chr2:171570800-171572600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:171570800-171572600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr2:171570800-171572600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
44	chr2:171570800-171574000	Bivalent/Poised TSS	HSMM	muscle
45	chr2:171571000-171572400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
46	chr2:171571000-171572600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:171571000-171572600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:171571000-171572800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
49	chr2:171571000-171572800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
50	chr2:171571000-171572800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum

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