Variant report

Variant	rs2287109
Chromosome Location	chr2:171574217-171574218
allele	A/C
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	TEAD4	chr2:171574127-171575775	HepG2	liver:	n/a	n/a
3	MAX	chr2:171567494-171574371	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
4	MBD4	chr2:171573282-171575454	HepG2	liver:	n/a	n/a
5	MAX	chr2:171567137-171574353	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
6	POLR2A	chr2:171571577-171574339	HepG2	liver:	n/a	n/a
7	E2F6	chr2:171572637-171574298	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr2:171572870-171574256	H1-hESC	embryonic stem cell:	n/a	n/a
9	HEY1	chr2:171566552-171576261	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
10	NFIC	chr2:171574118-171575194	HepG2	liver:	n/a	n/a
11	MYBL2	chr2:171573173-171574324	HepG2	liver:	n/a	n/a
12	HEY1	chr2:171566435-171575595	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
13	MBD4	chr2:171573317-171574225	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:171566818-171576833	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:171571636-171576275	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:171567743-171574223	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:171566701-171575246	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:171571166-171577125	HepG2	liver:	n/a	n/a
19	MAX	chr2:171572847-171574289	H1-hESC	embryonic stem cell:	n/a	n/a
20	SUZ12	chr2:171573448-171574233	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171571171..171574868-chr2:171624858..171628652,5	K562	blood:
2	chr2:171573568..171575819-chr2:171620402..171623627,3	K562	blood:

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

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10179149	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10181981	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10184230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10185519	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10188135	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10193894	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10200830	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10204585	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10211629	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10460355	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10460356	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930437	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11684810	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12472667	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12611849	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614245	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12618173	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12990209	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12994080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13009323	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13015956	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362487	0.84[ASN][1000 genomes]
rs1362491	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1420377	0.86[ASN][1000 genomes]
rs1420382	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1420384	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477060	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17694506	0.86[ASN][1000 genomes]
rs17750734	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1861463	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894917	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058726	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2216135	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2356232	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2883885	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28863322	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28892917	0.81[ASN][1000 genomes]
rs35294186	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233832	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667649	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667650	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667651	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4667652	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4667658	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4668302	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668303	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668304	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668305	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668306	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668312	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4668314	0.86[ASN][1000 genomes]
rs4668317	0.84[ASN][1000 genomes]
rs5003926	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5003927	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55806232	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58691943	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6433236	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433237	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433239	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433240	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433245	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66624589	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6717778	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6717785	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726174	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727988	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732964	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6741549	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746220	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6746374	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6751667	0.85[ASN][1000 genomes]
rs6751987	0.81[EUR][1000 genomes]
rs6756891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7556674	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563812	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7572599	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7582102	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7582425	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582430	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594247	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595158	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7608898	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs959463	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959464	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959465	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3324673	chr2:171572331-171574879	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171569400-171574400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:171569600-171574800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr2:171569600-171575600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:171570000-171575600	Bivalent/Poised TSS	HepG2	liver
5	chr2:171570000-171576200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:171570200-171574400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:171570200-171576200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:171570400-171576200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:171571800-171575200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:171571800-171577000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:171572200-171574400	Bivalent Enhancer	Stomach Mucosa	stomach
12	chr2:171572400-171574800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:171572400-171575000	Bivalent Enhancer	Fetal Thymus	thymus
14	chr2:171572800-171574400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr2:171572800-171574600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:171573600-171574400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
17	chr2:171573600-171574400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr2:171573600-171574400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
19	chr2:171573600-171575000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr2:171573800-171574800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:171574000-171574400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr2:171574000-171574400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:171574000-171574600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr2:171574000-171574600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:171574000-171574800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:171574000-171575000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
27	chr2:171574000-171620800	Weak transcription	Pancreas	Pancrea
28	chr2:171574200-171574400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
29	chr2:171574200-171574400	Bivalent Enhancer	Brain Germinal Matrix	brain
30	chr2:171574200-171574400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
31	chr2:171574200-171574600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:171574200-171574600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
33	chr2:171574200-171574600	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr2:171574200-171574800	Bivalent Enhancer	Primary T cells from cord blood	blood
35	chr2:171574200-171574800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
36	chr2:171574200-171574800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
37	chr2:171574200-171575000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:171574200-171575000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
39	chr2:171574200-171576000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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