Variant report

Variant	rs59168361
Chromosome Location	chr12:120529666-120529667
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	chr12:120529655-120529782	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:120529086-120529688	U87	brain:	n/a	n/a
5	POLR2A	chr12:120527520-120530522	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:120529643-120530434	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:120529354-120529821	A549	lung:	n/a	n/a
8	POLR2A	chr12:120529086-120529755	U87	brain:	n/a	n/a
9	POLR2A	chr12:120529664-120529755	Hela-S3	cervix:	n/a	n/a
10	NFIC	chr12:120528943-120529734	ECC-1	luminal epithelium:	n/a	chr12:120529342-120529370 chr12:120529279-120529296
11	POLR2A	chr12:120529378-120529692	MCF-7	breast:	n/a	n/a

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

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10128766	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10400498	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10400560	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10849731	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10849732	0.85[ASN][1000 genomes]
rs10849735	0.86[ASN][1000 genomes]
rs10849736	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11064987	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11064988	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11064996	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065003	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11833221	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12310269	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12310591	0.91[ASN][1000 genomes]
rs12313413	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12318774	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12320793	0.84[ASN][1000 genomes]
rs12322236	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12422923	0.91[ASN][1000 genomes]
rs16949901	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16949946	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16949961	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17841967	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239200	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239201	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239202	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239203	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239204	0.99[ASN][1000 genomes]
rs2283359	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283360	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283361	0.81[ASN][1000 genomes]
rs2286040	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28726166	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742042	0.83[AMR][1000 genomes]
rs4767869	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4767871	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767872	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4767875	0.91[ASN][1000 genomes]
rs4767876	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58272825	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60466490	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7298183	0.85[ASN][1000 genomes]
rs7298727	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7300023	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312971	0.91[ASN][1000 genomes]
rs7397339	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958402	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7958497	0.83[ASN][1000 genomes]
rs7965829	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7968557	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7978927	0.90[ASN][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:122 , 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	chr12:120525400-120529800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:120525400-120530200	Weak transcription	Left Ventricle	heart
5	chr12:120525400-120534200	Weak transcription	Right Atrium	heart
6	chr12:120525600-120529800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:120525600-120529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:120525600-120530000	Weak transcription	Adipose Nuclei	Adipose
9	chr12:120525600-120530000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:120525600-120530200	Weak transcription	Colonic Mucosa	Colon
11	chr12:120525600-120530200	Weak transcription	Right Ventricle	heart
12	chr12:120525600-120530400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:120525600-120530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:120525600-120530400	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:120525600-120531200	Weak transcription	Fetal Lung	lung
16	chr12:120525600-120531400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:120525600-120531600	Weak transcription	Aorta	Aorta
18	chr12:120525600-120531600	Weak transcription	Brain Angular Gyrus	brain
19	chr12:120525600-120531600	Weak transcription	K562	blood
20	chr12:120525600-120532200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:120525600-120532200	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:120525600-120532400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:120525600-120532400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:120525600-120532400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:120525600-120532400	Weak transcription	Ovary	ovary
26	chr12:120525600-120532400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:120525600-120533600	Weak transcription	Stomach Mucosa	stomach
28	chr12:120525600-120533600	Weak transcription	HSMMtube	muscle
29	chr12:120525600-120533600	Weak transcription	HUVEC	blood vessel
30	chr12:120525600-120533800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:120525600-120536000	Weak transcription	NHDF-Ad	bronchial
32	chr12:120525600-120539200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:120525800-120529800	Weak transcription	Brain Anterior Caudate	brain
35	chr12:120525800-120530000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:120525800-120530400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:120525800-120530400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:120525800-120530600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:120525800-120530600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:120525800-120530800	Weak transcription	HepG2	liver
41	chr12:120525800-120531000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:120525800-120531200	Weak transcription	Fetal Heart	heart
43	chr12:120525800-120532000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:120525800-120532200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:120525800-120532400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:120525800-120532400	Weak transcription	Osteobl	bone
47	chr12:120525800-120532600	Weak transcription	Liver	Liver
48	chr12:120525800-120533600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:120525800-120533800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:120525800-120536200	Weak transcription	Hela-S3	cervix

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