Variant report

Variant	rs10861479
Chromosome Location	chr12:106099565-106099566
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	chr12:106099560-106099710	HMEC	breast:	n/a	n/a
2	RAD21	chr12:106099471-106099867	MCF-7	breast:	n/a	chr12:106099640-106099659
3	CTCF	chr12:106099531-106099751	Kidney_OC	kidney:	n/a	n/a
4	CTCF	chr12:106099560-106099710	BJ	skin:	n/a	n/a
5	CTCF	chr12:106099489-106099795	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr12:106099560-106099710	AG09309	skin:	n/a	n/a
7	CTCF	chr12:106099527-106099782	A549	lung:	n/a	n/a
8	CTCF	chr12:106099500-106099650	HCT-116	colon:	n/a	n/a
9	CTCF	chr12:106099560-106099710	AG10803	skin:	n/a	n/a
10	RAD21	chr12:106099510-106099766	H1-hESC	embryonic stem cell:	n/a	chr12:106099640-106099659
11	CTCF	chr12:106099560-106099710	SAEC	small airway:	n/a	n/a
12	CTCF	chr12:106099504-106099806	Medullo	brain:	n/a	n/a
13	CTCF	chr12:106099368-106099899	MCF-7	breast:	n/a	n/a
14	CTCF	chr12:106099540-106099690	GM12864	blood:	n/a	n/a
15	CTCF	chr12:106099560-106099710	K562	blood:	n/a	n/a
16	CTCF	chr12:106099540-106099690	HPAF	blood vessel:	n/a	n/a
17	RAD21	chr12:106099411-106099862	H1-hESC	embryonic stem cell:	n/a	chr12:106099640-106099659
18	CTCF	chr12:106099560-106099710	GM12870	blood:	n/a	n/a
19	TCF12	chr12:106099512-106101093	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr12:106099560-106099710	GM12868	blood:	n/a	n/a
21	CTCF	chr12:106099540-106099690	GM12872	blood:	n/a	n/a
22	RAD21	chr12:106099556-106099674	K562	blood:	n/a	chr12:106099640-106099659
23	CTCF	chr12:106099540-106099690	GM12869	blood:	n/a	n/a
24	SMC3	chr12:106099216-106100498	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr12:106099412-106099838	HepG2	liver:	n/a	n/a
26	CTCF	chr12:106099535-106099792	GM10266	blood:	n/a	n/a
27	RAD21	chr12:106099439-106099775	GM12878	blood:	n/a	chr12:106099640-106099659
28	ELK1	chr12:106099543-106099636	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr12:106099540-106099690	HCM	heart:	n/a	n/a
30	CTCF	chr12:106099540-106099690	GM12870	blood:	n/a	n/a
31	ATF2	chr12:106099507-106099870	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr12:106099481-106099866	HepG2	liver:	n/a	chr12:106099640-106099659
33	CTCF	chr12:106099503-106099793	Pancreas_OC	pancreas:	n/a	n/a
34	CTCF	chr12:106099499-106099798	K562	blood:	n/a	n/a
35	CTCF	chr12:106099560-106099710	HRPEpiC	eye:	n/a	n/a
36	CTCF	chr12:106099518-106099757	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr12:106099532-106099786	MCF-7	breast:	n/a	n/a
38	CTCF	chr12:106099560-106099710	GM12871	blood:	n/a	n/a
39	CTCF	chr12:106099462-106099779	ECC-1	luminal epithelium:	n/a	n/a
40	RAD21	chr12:106099491-106099859	A549	lung:	n/a	chr12:106099640-106099659
41	CTCF	chr12:106099560-106099710	GM12875	blood:	n/a	n/a
42	ZNF143	chr12:106099482-106099819	K562	blood:	n/a	chr12:106099569-106099578
43	ZNF143	chr12:106099482-106099811	GM12878	blood:	n/a	chr12:106099569-106099578
44	TEAD4	chr12:106099451-106099852	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr12:106099498-106099978	GM12878	blood:	n/a	n/a
46	IRF1	chr12:106099503-106099723	K562	blood:	n/a	chr12:106099553-106099567 chr12:106099554-106099566
47	CTCF	chr12:106099458-106099731	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr12:106099560-106099710	HCFaa	heart:	n/a	n/a
49	CTCF	chr12:106099369-106099917	MCF-7	breast:	n/a	n/a
50	RAD21	chr12:106099494-106099860	SK-N-SH_RA	brain:	n/a	chr12:106099640-106099659

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106099358..106100248-chr12:106529662..106530556,3	K562	blood:
2	chr12:105814204..105815049-chr12:106099199..106100140,3	MCF-7	breast:

Variant related genes	Relation type
CASC18	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11112686	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133311	1.00[JPT][hapmap]

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	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899503	chr12:106021477-106175903	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1047810	chr12:106067049-106246582	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1040261	chr12:106068992-106246582	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv899504	chr12:106095906-106135942	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106095200-106099600	Weak transcription	Aorta	Aorta
2	chr12:106095800-106099600	Weak transcription	Right Atrium	heart
3	chr12:106096600-106099600	Weak transcription	Fetal Brain Male	brain
4	chr12:106097400-106099800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:106097400-106101000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr12:106098000-106100600	Enhancers	Fetal Muscle Trunk	muscle
7	chr12:106098000-106101200	Enhancers	Fetal Heart	heart
8	chr12:106098000-106101400	Enhancers	Fetal Muscle Leg	muscle
9	chr12:106098200-106099600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:106098200-106099800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:106098400-106099600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:106098400-106099800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:106098400-106100200	Enhancers	Fetal Lung	lung
14	chr12:106098400-106101400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:106098600-106099800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:106098600-106099800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:106098600-106100000	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr12:106098600-106100200	Enhancers	Lung	lung
19	chr12:106098600-106101600	Enhancers	HSMMtube	muscle
20	chr12:106098800-106099800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:106098800-106099800	Weak transcription	Left Ventricle	heart
22	chr12:106098800-106099800	Weak transcription	Right Ventricle	heart
23	chr12:106098800-106101400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:106098800-106101400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:106099000-106099600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr12:106099000-106100000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:106099000-106100200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:106099000-106100200	Enhancers	Brain Cingulate Gyrus	brain
29	chr12:106099000-106101000	Enhancers	Psoas Muscle	Psoas
30	chr12:106099000-106101200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:106099200-106099600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:106099200-106099600	Weak transcription	Brain Angular Gyrus	brain
33	chr12:106099200-106100000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:106099200-106100600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:106099200-106100600	Enhancers	HUVEC	blood vessel
36	chr12:106099200-106101400	Enhancers	HSMM	muscle
37	chr12:106099400-106100400	Enhancers	Brain Hippocampus Middle	brain
38	chr12:106099400-106100800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr12:106099400-106101000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:106099400-106101000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:106099400-106101400	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links