Variant report

Variant	rs11065018
Chromosome Location	chr12:120529307-120529308
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	NFIC	chr12:120528941-120529723	SK-N-SH	brain:	n/a	chr12:120529342-120529370 chr12:120529279-120529296
2	NFIC	chr12:120528973-120529695	ECC-1	luminal epithelium:	n/a	chr12:120529342-120529370 chr12:120529279-120529296
3	POLR2A	chr12:120529290-120529445	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:120529218-120529444	HCT-116	colon:	n/a	n/a
5	NFIC	chr12:120529061-120529579	SK-N-SH	brain:	n/a	chr12:120529342-120529370 chr12:120529279-120529296
6	POLR2A	chr12:120529086-120529688	U87	brain:	n/a	n/a
7	POLR2A	chr12:120527520-120530522	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr12:120529274-120529434	ProgFib	skin:	n/a	n/a
9	POLR2A	chr12:120529086-120529755	U87	brain:	n/a	n/a
10	NFIC	chr12:120528943-120529734	ECC-1	luminal epithelium:	n/a	chr12:120529342-120529370 chr12:120529279-120529296
11	POLR2A	chr12:120529217-120529471	HCT-116	colon:	n/a	n/a
12	POLR2A	chr12:120528251-120529354	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr12:120529299-120529551	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120528003..120529551-chr12:120530435..120532991,2	K562	blood:
2	chr12:120529252..120531739-chr12:120728322..120731564,3	MCF-7	breast:
3	chr12:120528996..120531217-chr12:120552975..120554934,2	MCF-7	breast:
4	chr12:120524977..120526839-chr12:120528697..120530517,2	MCF-7	breast:

Variant related genes	Relation type
CCDC64	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10744747	0.80[ASN][1000 genomes]
rs11064986	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11064998	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11065004	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065014	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065017	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311327	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12320072	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240311	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2393570	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3742044	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3759399	0.95[ASN][1000 genomes]
rs3852586	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3852588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3886910	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3999575	0.96[ASN][1000 genomes]
rs4105713	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4351876	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4767873	0.80[EUR][1000 genomes]
rs6490278	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6490280	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6490281	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6490283	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6490284	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7295717	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7305625	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7306739	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312811	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7314959	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956436	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7960725	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7961738	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7962812	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7971249	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7977281	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active 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	99 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120524800-120531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:120525000-120530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:120525400-120529600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:120525400-120529800	Weak transcription	Fetal Intestine Large	intestine
5	chr12:120525400-120530200	Weak transcription	Left Ventricle	heart
6	chr12:120525400-120534200	Weak transcription	Right Atrium	heart
7	chr12:120525600-120529400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:120525600-120529400	Weak transcription	Fetal Stomach	stomach
9	chr12:120525600-120529400	Weak transcription	HSMM	muscle
10	chr12:120525600-120529400	Weak transcription	NHLF	lung
11	chr12:120525600-120529600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:120525600-120529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:120525600-120529800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:120525600-120529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:120525600-120530000	Weak transcription	Adipose Nuclei	Adipose
16	chr12:120525600-120530000	Weak transcription	Brain Substantia Nigra	brain
17	chr12:120525600-120530200	Weak transcription	Colonic Mucosa	Colon
18	chr12:120525600-120530200	Weak transcription	Right Ventricle	heart
19	chr12:120525600-120530400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:120525600-120530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:120525600-120530400	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:120525600-120531200	Weak transcription	Fetal Lung	lung
23	chr12:120525600-120531400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:120525600-120531600	Weak transcription	Aorta	Aorta
25	chr12:120525600-120531600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:120525600-120531600	Weak transcription	K562	blood
27	chr12:120525600-120532200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:120525600-120532200	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:120525600-120532400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:120525600-120532400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:120525600-120532400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:120525600-120532400	Weak transcription	Ovary	ovary
33	chr12:120525600-120532400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:120525600-120533600	Weak transcription	Stomach Mucosa	stomach
35	chr12:120525600-120533600	Weak transcription	HSMMtube	muscle
36	chr12:120525600-120533600	Weak transcription	HUVEC	blood vessel
37	chr12:120525600-120533800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:120525600-120536000	Weak transcription	NHDF-Ad	bronchial
39	chr12:120525600-120539200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:120525800-120529400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:120525800-120529600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:120525800-120529600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:120525800-120529800	Weak transcription	Brain Anterior Caudate	brain
45	chr12:120525800-120530000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:120525800-120530400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr12:120525800-120530400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:120525800-120530600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:120525800-120530600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:120525800-120530800	Weak transcription	HepG2	liver

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