Variant report

Variant	rs2283345
Chromosome Location	chr12:48109024-48109025
allele	C/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	chr12:48109024-48109589	K562	blood:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
2	RAD21	chr12:48109014-48109536	HepG2	liver:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276
3	CTCF	chr12:48109008-48109515	A549	lung:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
4	CTCF	chr12:48108763-48109689	A549	lung:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
5	RAD21	chr12:48109018-48109618	ECC-1	luminal epithelium:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
6	RAD21	chr12:48109000-48109622	MCF-7	breast:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
7	CTCF	chr12:48108947-48109553	HCT-116	colon:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
8	FOXA2	chr12:48108947-48109568	A549	lung:	n/a	n/a
9	RAD21	chr12:48108989-48109613	H1-hESC	embryonic stem cell:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
10	CTCF	chr12:48108901-48109873	HCT-116	colon:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
11	RAD21	chr12:48108901-48109738	HCT-116	colon:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
12	CTCF	chr12:48108823-48109568	IMR90	lung:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
13	SMC3	chr12:48108800-48109553	GM12878	blood:	n/a	chr12:48109264-48109274 chr12:48109260-48109274
14	RAD21	chr12:48108961-48109630	MCF-7	breast:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
15	RAD21	chr12:48108959-48109798	SK-N-SH	brain:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
16	CTCF	chr12:48108920-48109070	GM12871	blood:	n/a	n/a
17	RAD21	chr12:48108846-48109677	HCT-116	colon:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
18	FOXA1	chr12:48109017-48109482	HepG2	liver:	n/a	n/a
19	RAD21	chr12:48108971-48109714	ECC-1	luminal epithelium:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
20	RAD21	chr12:48108971-48109630	A549	lung:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
21	CTCF	chr12:48108880-48109030	HPAF	blood vessel:	n/a	n/a
22	CTCF	chr12:48109012-48109445	ECC-1	luminal epithelium:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
23	CTCF	chr12:48108981-48109552	MCF-7	breast:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
24	SMC3	chr12:48108668-48109760	SK-N-SH	brain:	n/a	chr12:48109264-48109274 chr12:48109260-48109274
25	SMC3	chr12:48108992-48109490	HepG2	liver:	n/a	chr12:48109264-48109274 chr12:48109260-48109274
26	RAD21	chr12:48109001-48109579	SK-N-SH_RA	brain:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
27	CTCF	chr12:48108938-48109608	MCF-7	breast:	n/a	chr12:48109258-48109276 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
28	CTCF	chr12:48108771-48110151	SK-N-SH	brain:	n/a	chr12:48109258-48109276 chr12:48109887-48109900 chr12:48109259-48109275 chr12:48109261-48109274 chr12:48109260-48109281
29	RAD21	chr12:48109015-48109646	A549	lung:	n/a	chr12:48109259-48109278 chr12:48109262-48109275 chr12:48109264-48109274 chr12:48109264-48109276 chr12:48109541-48109550
30	CTCF	chr12:48108880-48109030	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48108686..48109785-chr12:48232014..48233018,9	MCF-7	breast:
2	chr12:48107776..48110722-chr12:48159579..48161577,2	K562	blood:
3	chr12:48108449..48110795-chr12:48232871..48234613,2	K562	blood:
4	chr12:48108810..48109754-chr12:48172755..48173734,6	K562	blood:
5	chr12:48109020..48109676-chr12:48117627..48118375,2	K562	blood:
6	chr12:48108711..48109786-chr12:48173181..48173711,3	MCF-7	breast:
7	chr12:48108161..48111101-chr12:48229795..48232541,2	K562	blood:
8	chr12:48108886..48110989-chr12:48118546..48121224,2	MCF-7	breast:
9	chr12:48108894..48109761-chr12:48170471..48172411,6	K562	blood:
10	chr12:48108886..48109697-chr12:48230502..48231168,3	K562	blood:
11	chr12:48108807..48109517-chr12:48137483..48138335,4	MCF-7	breast:
12	chr12:48108739..48111513-chr12:48143992..48146721,2	MCF-7	breast:
13	chr12:48108762..48109744-chr12:48166665..48167534,3	MCF-7	breast:
14	chr12:48108819..48109771-chr12:48342972..48343902,5	K562	blood:
15	chr12:48106450..48109215-chr12:48211629..48213525,2	MCF-7	breast:
16	chr12:48108819..48109698-chr12:48232035..48232888,2	MCF-7	breast:
17	chr12:48107756..48109662-chr12:48167416..48168986,2	K562	blood:
18	chr12:48108389..48110707-chr12:48231215..48233864,2	MCF-7	breast:
19	chr12:48108347..48109699-chr12:48160633..48161575,5	K562	blood:
20	chr12:48108354..48111166-chr12:48231258..48232998,20	K562	blood:
21	chr12:48098499..48101428-chr12:48108711..48111511,2	MCF-7	breast:
22	chr12:48108589..48112284-chr12:48169450..48173129,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257433	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000111405	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10875683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168187	0.86[ASN][1000 genomes]
rs11168194	0.81[JPT][hapmap]
rs11168212	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168219	0.86[ASN][1000 genomes]
rs11168220	0.82[ASN][1000 genomes]
rs11830795	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11834770	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1235152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426774	0.85[CEU][hapmap]
rs12810487	0.85[CEU][hapmap]
rs12812460	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12812960	0.94[ASN][1000 genomes]
rs12818241	0.85[CEU][hapmap]
rs12819759	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12820269	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12828238	0.86[ASN][1000 genomes]
rs2003471	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074531	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074532	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238144	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2239188	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3764015	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764016	0.99[ASN][1000 genomes]
rs3764018	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764019	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764020	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505143	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4537844	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580635	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580636	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133585	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726588	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302276	0.94[ASN][1000 genomes]
rs7306556	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7967336	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967546	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976708	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48100000-48109200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:48100000-48111200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:48100800-48109400	Weak transcription	HSMM	muscle
4	chr12:48101000-48109200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:48101000-48109200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:48101200-48109200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:48101400-48109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:48101400-48111000	Weak transcription	Colonic Mucosa	Colon
9	chr12:48101400-48111200	Weak transcription	Small Intestine	intestine
10	chr12:48101800-48111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:48102000-48109200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:48102800-48125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:48103000-48109200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:48103000-48109400	Weak transcription	Primary T cells from cord blood	blood
15	chr12:48103200-48111200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:48103400-48111000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:48103800-48109200	Weak transcription	K562	blood
18	chr12:48104600-48113000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:48104800-48109400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:48105600-48111200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:48106200-48112600	Enhancers	Ovary	ovary
22	chr12:48106600-48111200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:48108000-48109400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:48108200-48109200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr12:48108200-48109400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:48108200-48112400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:48108600-48109200	Enhancers	Adipose Nuclei	Adipose
28	chr12:48108600-48109200	Enhancers	Colon Smooth Muscle	Colon
29	chr12:48108600-48112400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:48108800-48109200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:48108800-48109200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:48108800-48109200	Enhancers	Liver	Liver
33	chr12:48108800-48109200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr12:48108800-48109200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr12:48108800-48109400	Enhancers	Brain Anterior Caudate	brain
36	chr12:48108800-48109600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:48108800-48109600	Enhancers	Primary B cells from cord blood	blood
38	chr12:48108800-48109600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr12:48108800-48109600	Enhancers	GM12878-XiMat	blood
40	chr12:48108800-48109800	Enhancers	Fetal Lung	lung
41	chr12:48108800-48111200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr12:48108800-48111200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:48108800-48112200	Enhancers	Brain Angular Gyrus	brain
44	chr12:48108800-48112200	Enhancers	Fetal Muscle Trunk	muscle
45	chr12:48108800-48112600	Enhancers	Brain Cingulate Gyrus	brain
46	chr12:48108800-48112600	Enhancers	Fetal Muscle Leg	muscle
47	chr12:48108800-48112600	Enhancers	Fetal Stomach	stomach
48	chr12:48108800-48112600	Enhancers	Left Ventricle	heart
49	chr12:48108800-48112600	Enhancers	Right Atrium	heart
50	chr12:48108800-48112600	Enhancers	Right Ventricle	heart

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