Variant report

Variant	rs12997222
Chromosome Location	chr2:57987201-57987202
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	CTCF	chr2:57987080-57987230	HCFaa	heart:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
2	CHD2	chr2:57987032-57987329	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr2:57986886-57987282	HCT-116	colon:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
4	FOXP2	chr2:57987028-57987279	SK-N-MC	brain:	n/a	n/a
5	GATA3	chr2:57986872-57987345	T-47D	breast:	n/a	n/a
6	CTCF	chr2:57987060-57987210	GM12866	blood:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
7	MAX	chr2:57986999-57987390	NB4	blood:	n/a	n/a
8	TBL1XR1	chr2:57987019-57987272	GM12878	blood:	n/a	n/a
9	CTCF	chr2:57986957-57987316	T-47D	breast:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
10	EP300	chr2:57987005-57987319	GM12878	blood:	n/a	n/a
11	CTCF	chr2:57987005-57987256	GM10248	blood:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
12	RCOR1	chr2:57986987-57987338	K562	blood:	n/a	n/a
13	GATA2	chr2:57986732-57987515	SH-SY5Y	brain:	n/a	n/a
14	FOXM1	chr2:57986775-57987438	GM12878	blood:	n/a	n/a
15	REST	chr2:57986990-57987410	U87	brain:	n/a	n/a
16	RAD21	chr2:57986860-57987506	MCF-7	breast:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
17	POU2F2	chr2:57987039-57987216	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr2:57987067-57987407	K562	blood:	n/a	n/a
19	CTCF	chr2:57987080-57987230	NHEK	skin:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
20	MAX	chr2:57987017-57987459	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZC3H11A	chr2:57986991-57987289	K562	blood:	n/a	n/a
22	YY1	chr2:57987018-57987261	SK-N-SH_RA	brain:	n/a	chr2:57987137-57987156
23	CTCF	chr2:57987060-57987210	HepG2	liver:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
24	MAX	chr2:57987006-57987430	K562	blood:	n/a	n/a
25	RAD21	chr2:57986923-57987390	ECC-1	luminal epithelium:	n/a	chr2:57987139-57987153 chr2:57987143-57987155 chr2:57987101-57987113 chr2:57987140-57987147 chr2:57987138-57987157
26	SIN3A	chr2:57986913-57987326	H1-hESC	embryonic stem cell:	n/a	n/a
27	ATF3	chr2:57986897-57987440	A549	lung:	n/a	n/a
28	CTCF	chr2:57987060-57987210	NB4	blood:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
29	CTCF	chr2:57986991-57987344	A549	lung:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
30	CTCF	chr2:57986953-57987346	H1-hESC	embryonic stem cell:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
31	CTCF	chr2:57987100-57987250	GM12873	blood:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
32	E2F4	chr2:57987048-57987239	GM12878	blood:	n/a	chr2:57987204-57987211
33	SMC3	chr2:57986934-57987412	Hela-S3	cervix:	n/a	chr2:57987139-57987153
34	CTCF	chr2:57987060-57987210	NHEK	skin:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
35	CHD2	chr2:57987160-57987349	K562	blood:	n/a	n/a
36	CTCF	chr2:57986981-57987300	NHEK	skin:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
37	POU2F2	chr2:57987015-57987378	GM12891	blood:	n/a	n/a
38	CTCF	chr2:57987060-57987210	HPAF	blood vessel:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
39	MAZ	chr2:57986913-57987463	IMR90	lung:	n/a	n/a
40	YY1	chr2:57986984-57987452	GM12878	blood:	n/a	chr2:57987137-57987156
41	CTCF	chr2:57987080-57987230	SAEC	small airway:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
42	CTCF	chr2:57987060-57987210	AG09309	skin:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
43	MAX	chr2:57987008-57987313	HepG2	liver:	n/a	n/a
44	CUX1	chr2:57987077-57987289	K562	blood:	n/a	n/a
45	SMC3	chr2:57986948-57987521	HepG2	liver:	n/a	chr2:57987139-57987153
46	CTCF	chr2:57987013-57987270	LNCaP	prostate:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
47	CTCF	chr2:57987027-57987311	A549	lung:	n/a	chr2:57987139-57987160 chr2:57987138-57987154 chr2:57987137-57987155 chr2:57987142-57987150
48	IRF4	chr2:57986965-57987366	GM12878	blood:	n/a	n/a
49	YY1	chr2:57987033-57987448	GM12878	blood:	n/a	chr2:57987137-57987156
50	YY1	chr2:57986999-57987374	GM12892	blood:	n/a	chr2:57987137-57987156

No.	Distal block	Cell Line	Cell type
1	chr2:57986668..57987445-chr2:58674884..58675821,3	K562	blood:
2	chr2:57986735..57987942-chr2:58674900..58675939,5	MCF-7	breast:
3	chr2:57947756..57948609-chr2:57986675..57987249,2	MCF-7	breast:
4	chr2:57986795..57987623-chr2:58674835..58675860,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271615	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10204616	0.90[AMR][1000 genomes]
rs1040224	0.80[JPT][hapmap]
rs1040225	0.81[JPT][hapmap]
rs10496078	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496079	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865304	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1106302	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11898858	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713358	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12990792	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1402398	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1460255	0.81[AMR][1000 genomes]
rs1568450	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1589407	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2090793	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2204019	0.84[ASN][1000 genomes]
rs2465804	0.80[JPT][hapmap]
rs2678870	0.80[JPT][hapmap]
rs2678880	0.82[CEU][hapmap]
rs2678901	0.81[JPT][hapmap]
rs2678903	0.81[JPT][hapmap]
rs2678905	0.81[JPT][hapmap]
rs2678906	0.80[JPT][hapmap]
rs2678908	0.82[CEU][hapmap]
rs2683614	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2683616	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2683619	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683620	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683622	0.83[ASN][1000 genomes]
rs2683625	0.88[ASN][1000 genomes]
rs2683628	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2683629	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2716998	0.82[ASN][1000 genomes]
rs2716999	0.83[ASN][1000 genomes]
rs2717001	0.82[CEU][hapmap]
rs2717002	0.82[CEU][hapmap]
rs2717004	0.80[JPT][hapmap]
rs2717006	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs2717018	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2717019	0.80[JPT][hapmap]
rs2717043	0.80[JPT][hapmap]
rs2717048	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2717068	0.82[EUR][1000 genomes]
rs2717075	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2947350	0.82[ASN][1000 genomes]
rs2947351	0.83[ASN][1000 genomes]
rs2953437	0.83[ASN][1000 genomes]
rs2953438	0.84[ASN][1000 genomes]
rs2953439	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2953441	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2953443	0.88[ASN][1000 genomes]
rs3886275	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4296411	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4672223	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545663	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545664	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545665	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66490669	0.84[EUR][1000 genomes]
rs6730037	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6737913	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6756221	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6761347	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561842	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7588492	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598169	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs970941	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874197	chr2:57978858-58068741	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834148	chr2:57979661-58119213	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57985400-57987400	Enhancers	H1 Cell Line	embryonic stem cell
2	chr2:57985400-57988400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:57985600-57987400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:57986200-57987800	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:57986200-57987800	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr2:57986400-57987400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:57986400-57987400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:57986400-57987400	Enhancers	Pancreas	Pancrea
9	chr2:57986400-57987800	Active TSS	Brain Substantia Nigra	brain
10	chr2:57986400-57988000	Active TSS	Brain Angular Gyrus	brain
11	chr2:57986600-57987400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:57986600-57987400	Bivalent Enhancer	HMEC	breast
13	chr2:57986600-57987400	Enhancers	NHEK	skin
14	chr2:57986600-57987400	Enhancers	NHLF	lung
15	chr2:57986600-57987600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:57986600-57987600	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr2:57986600-57988000	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:57986600-57988000	Enhancers	Fetal Lung	lung
19	chr2:57986800-57987400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:57986800-57987400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:57986800-57987400	Enhancers	Left Ventricle	heart
22	chr2:57986800-57987400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:57986800-57987400	Active TSS	K562	blood
24	chr2:57986800-57987400	Active TSS	NH-A	brain
25	chr2:57986800-57987600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:57986800-57987600	Active TSS	Brain Hippocampus Middle	brain
27	chr2:57986800-57987600	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr2:57986800-57987600	Active TSS	Rectal Smooth Muscle	rectum
29	chr2:57986800-57987600	Flanking Active TSS	Osteobl	bone
30	chr2:57986800-57987800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:57986800-57987800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:57986800-57987800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr2:57986800-57987800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:57986800-57987800	Enhancers	Fetal Heart	heart
35	chr2:57986800-57987800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:57987000-57987400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:57987000-57987400	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:57987000-57987400	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr2:57987000-57987400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr2:57987000-57987400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:57987000-57987400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:57987000-57987400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:57987000-57987400	Flanking Active TSS	Ovary	ovary
44	chr2:57987000-57987400	Transcr. at gene 5' and 3'	Right Atrium	heart
45	chr2:57987000-57987400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:57987000-57987400	Flanking Active TSS	Thymus	Thymus
47	chr2:57987000-57987400	Active TSS	A549	lung
48	chr2:57987000-57987400	Flanking Active TSS	Hela-S3	cervix
49	chr2:57987000-57987600	Active TSS	Primary T cells from cord blood	blood
50	chr2:57987000-57987600	Active TSS	Primary hematopoietic stem cells short term culture	blood

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