Variant report

Variant	rs12299143
Chromosome Location	chr12:120752722-120752723
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	chr12:120751841-120752728	A549	lung:	n/a	chr12:120752219-120752240 chr12:120752217-120752235

No.	Distal block	Cell Line	Cell type
1	chr12:120727833..120732436-chr12:120750797..120758239,21	K562	blood:
2	chr12:120727172..120733111-chr12:120749358..120767260,47	MCF-7	breast:
3	chr12:120737630..120743237-chr12:120750628..120756565,17	MCF-7	breast:
4	chr12:120751950..120753802-chr12:120875865..120878034,2	K562	blood:
5	chr12:120727224..120732436-chr12:120750439..120758135,29	K562	blood:
6	chr12:120663204..120669945-chr12:120752406..120756905,6	K562	blood:

Variant related genes	Relation type
RNU6-1088P	TF binding region
ENSG00000111775	Chromatin interaction
ENSG00000111780	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000089159	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000089163	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12423303	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12424233	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12424555	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425936	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12426900	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12427069	0.93[EUR][1000 genomes]
rs12427095	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16950044	0.93[EUR][1000 genomes]
rs16950047	0.93[EUR][1000 genomes]
rs16950058	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16950061	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16950065	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16950101	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2238158	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2238161	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2464296	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2522140	0.88[EUR][1000 genomes]
rs2701643	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2905543	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3847967	0.81[EUR][1000 genomes]
rs3847968	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3847969	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3898618	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56237802	0.83[ASN][1000 genomes]
rs5634	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56733641	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57141366	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57279831	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57384430	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58232894	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59447311	0.92[EUR][1000 genomes]
rs59768240	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60176939	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60731947	0.93[EUR][1000 genomes]
rs61140476	0.83[EUR][1000 genomes]
rs61592165	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61665022	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61748115	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7960401	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977875	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9657936	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9657937	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9657941	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9657942	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9657948	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
3	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
4	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
5	nsv560435	chr12:120695141-120769657	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
6	nsv899556	chr12:120695141-120779931	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120740400-120754600	Weak transcription	Stomach Mucosa	stomach
2	chr12:120740400-120754800	Weak transcription	Spleen	Spleen
3	chr12:120740600-120754600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:120740600-120754800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:120741000-120754200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:120741000-120754200	Weak transcription	Placenta	Placenta
7	chr12:120741000-120754400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:120741000-120754400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:120741000-120754600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:120741000-120754600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:120741000-120754600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:120741000-120754600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:120741000-120754600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:120741000-120754600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:120741000-120754600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:120741000-120754600	Weak transcription	Brain Anterior Caudate	brain
17	chr12:120741000-120754600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:120741000-120754600	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:120741000-120754600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:120741000-120754600	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:120741000-120754600	Weak transcription	Fetal Heart	heart
22	chr12:120741000-120754600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:120741000-120754600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:120741000-120754600	Weak transcription	Right Ventricle	heart
25	chr12:120741000-120754600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:120741200-120753800	Weak transcription	Liver	Liver
27	chr12:120741200-120754200	Weak transcription	Fetal Brain Female	brain
28	chr12:120741200-120754600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:120741400-120754600	Weak transcription	Brain Germinal Matrix	brain
30	chr12:120741400-120754600	Weak transcription	Thymus	Thymus
31	chr12:120741600-120754000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:120741600-120754200	Weak transcription	Lung	lung
33	chr12:120741600-120754600	Weak transcription	Brain Substantia Nigra	brain
34	chr12:120741800-120754600	Weak transcription	Left Ventricle	heart
35	chr12:120742000-120754600	Weak transcription	Fetal Brain Male	brain
36	chr12:120742000-120754600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:120742200-120754600	Weak transcription	Fetal Stomach	stomach
38	chr12:120742600-120754600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:120742600-120754600	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:120743600-120754600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:120746800-120754600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:120750600-120754400	Weak transcription	K562	blood
43	chr12:120750800-120754400	Weak transcription	HepG2	liver
44	chr12:120752400-120753200	Weak transcription	Pancreas	Pancrea
45	chr12:120752600-120754600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:120752600-120754600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:120752600-120754600	Weak transcription	A549	lung

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