Variant report

Variant	rs11169265
Chromosome Location	chr12:50464254-50464255
allele	A/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	chr12:50464224-50464664	T-47D	breast:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
2	SMC3	chr12:50464197-50464750	Hela-S3	cervix:	n/a	chr12:50464455-50464469
3	ELF1	chr12:50464197-50464773	A549	lung:	n/a	chr12:50464545-50464558 chr12:50464420-50464431
4	CTCF	chr12:50464254-50464679	GM12878	blood:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
5	CTCF	chr12:50464123-50464790	MCF-7	breast:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
6	CTCF	chr12:50464227-50464651	K562	blood:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
7	SMC3	chr12:50463885-50464906	SK-N-SH	brain:	n/a	chr12:50464455-50464469
8	RAD21	chr12:50464154-50464753	A549	lung:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
9	ZNF263	chr12:50464189-50464858	HEK293-T-REx	kidney:	n/a	chr12:50464564-50464573
10	RAD21	chr12:50464215-50464640	GM12878	blood:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
11	GTF2F1	chr12:50464213-50464680	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr12:50464235-50464653	H1-hESC	embryonic stem cell:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
13	MAZ	chr12:50464249-50464831	Hela-S3	cervix:	n/a	chr12:50464718-50464727
14	GABPA	chr12:50464182-50464877	A549	lung:	n/a	n/a
15	POLR2A	chr12:50464211-50464690	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr12:50464069-50464749	HCT-116	colon:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
17	CTCF	chr12:50464247-50464630	Spleen_OC	spleen:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
18	RAD21	chr12:50464232-50464643	H1-hESC	embryonic stem cell:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
19	HCFC1	chr12:50464226-50464766	K562	blood:	n/a	n/a
20	CTCF	chr12:50464081-50464654	GM19239	blood:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
21	CTCF	chr12:50464090-50464650	GM12892	blood:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
22	CTCF	chr12:50464116-50464652	GM19240	blood:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
23	RAD21	chr12:50464204-50464692	MCF-7	breast:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
24	CTCF	chr12:50463756-50464934	SK-N-SH	brain:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
25	CTCF	chr12:50464146-50464638	A549	lung:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
26	SMC3	chr12:50464234-50464856	K562	blood:	n/a	chr12:50464455-50464469
27	CTCF	chr12:50464197-50464595	HepG2	liver:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
28	RAD21	chr12:50464236-50464655	SK-N-SH_RA	brain:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
29	CBX3	chr12:50464114-50465062	K562	blood:	n/a	n/a
30	MAX	chr12:50464166-50464643	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:50464161-50464700	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:50464136-50464260	MCF-7	breast:	n/a	n/a
33	CTCF	chr12:50464124-50464759	MCF-7	breast:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
34	BHLHE40	chr12:50464207-50464617	K562	blood:	n/a	n/a
35	RAD21	chr12:50464220-50464632	HepG2	liver:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
36	ELK1	chr12:50464242-50464626	Hela-S3	cervix:	n/a	n/a
37	SMC3	chr12:50464248-50464665	GM12878	blood:	n/a	chr12:50464455-50464469
38	RAD21	chr12:50464232-50464592	K562	blood:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
39	CTCF	chr12:50464253-50464624	ProgFib	skin:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
40	CTCF	chr12:50464098-50464651	GM12891	blood:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
41	MAFK	chr12:50464206-50464604	Hela-S3	cervix:	n/a	n/a
42	GABPA	chr12:50464089-50464839	MCF-7	breast:	n/a	n/a
43	RAD21	chr12:50463936-50465125	SK-N-SH	brain:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50465016-50465029 chr12:50464461-50464468
44	JUND	chr12:50464246-50464786	K562	blood:	n/a	n/a
45	CTCF	chr12:50464209-50464662	H1-hESC	embryonic stem cell:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468
46	SIN3AK20	chr12:50464237-50464558	SK-N-SH	brain:	n/a	n/a
47	CHD2	chr12:50464241-50464518	GM12878	blood:	n/a	n/a
48	YY1	chr12:50464246-50464632	K562	blood:	n/a	n/a
49	RAD21	chr12:50463930-50464793	ECC-1	luminal epithelium:	n/a	chr12:50464457-50464466 chr12:50464453-50464465 chr12:50464451-50464470 chr12:50464461-50464468
50	CTCF	chr12:50464234-50464645	T-47D	breast:	n/a	chr12:50464454-50464470 chr12:50464448-50464469 chr12:50464458-50464466 chr12:50464453-50464471 chr12:50464455-50464468

No.	Distal block	Cell Line	Cell type
1	chr12:50360101..50361853-chr12:50463828..50465034,15	K562	blood:
2	chr12:50367709..50369586-chr12:50462445..50464458,2	MCF-7	breast:
3	chr12:50461826..50464798-chr12:50477927..50479451,2	K562	blood:
4	chr12:50452088..50458692-chr12:50460164..50465883,8	K562	blood:
5	chr12:50450859..50453547-chr12:50463168..50465511,2	MCF-7	breast:
6	chr12:50360423..50362281-chr12:50463512..50464987,20	MCF-7	breast:
7	chr12:50360531..50361497-chr12:50464033..50464946,8	MCF-7	breast:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000066117	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000086159	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10082763	1.00[ASN][1000 genomes]
rs11169267	0.89[AFR][1000 genomes]
rs12296518	0.96[AFR][1000 genomes]
rs12313064	0.82[AFR][1000 genomes]
rs2307080	1.00[ASW][hapmap];1.00[CHD][hapmap];0.80[YRI][hapmap]
rs2307083	1.00[ASN][1000 genomes]
rs3741561	1.00[ASN][1000 genomes]
rs61355003	0.83[AFR][1000 genomes]
rs629874	1.00[ASN][1000 genomes]
rs9805064	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised 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 miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50459600-50465000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:50460600-50465800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:50460600-50466000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:50460600-50469200	Weak transcription	Psoas Muscle	Psoas
6	chr12:50460600-50469400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:50460800-50469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:50461000-50465600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:50461000-50468800	Weak transcription	HSMMtube	muscle
10	chr12:50463800-50464800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:50463800-50464800	Enhancers	Brain Anterior Caudate	brain
12	chr12:50463800-50464800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:50463800-50464800	Enhancers	Colon Smooth Muscle	Colon
14	chr12:50463800-50464800	Enhancers	Fetal Brain Male	brain
15	chr12:50463800-50464800	Enhancers	Fetal Intestine Large	intestine
16	chr12:50463800-50465000	Genic enhancers	Fetal Brain Female	brain
17	chr12:50464000-50464400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:50464000-50464400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:50464000-50464400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:50464000-50464400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:50464000-50464400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:50464000-50464400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr12:50464000-50464400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr12:50464000-50464400	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr12:50464000-50464400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:50464000-50464400	Enhancers	Brain Substantia Nigra	brain
27	chr12:50464000-50464400	Enhancers	Duodenum Mucosa	Duodenum
28	chr12:50464000-50464400	Enhancers	Fetal Heart	heart
29	chr12:50464000-50464400	Enhancers	Fetal Kidney	kidney
30	chr12:50464000-50464400	Enhancers	Fetal Lung	lung
31	chr12:50464000-50464400	Enhancers	Lung	lung
32	chr12:50464000-50464400	Enhancers	Pancreas	Pancrea
33	chr12:50464000-50464400	Enhancers	Right Atrium	heart
34	chr12:50464000-50464400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr12:50464000-50464400	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr12:50464000-50464400	Flanking Active TSS	Hela-S3	cervix
37	chr12:50464000-50464400	Enhancers	HepG2	liver
38	chr12:50464000-50464400	Enhancers	Osteobl	bone
39	chr12:50464000-50464600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:50464000-50464600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:50464000-50464600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:50464000-50464600	Enhancers	Liver	Liver
43	chr12:50464000-50464600	Enhancers	Ovary	ovary
44	chr12:50464000-50464800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:50464000-50464800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:50464000-50464800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:50464000-50464800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:50464000-50464800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:50464000-50464800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:50464000-50464800	Enhancers	Brain Cingulate Gyrus	brain

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