Variant report

Variant	rs12404652
Chromosome Location	chr1:78404941-78404942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:78404782-78405476	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:78404190-78405415	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:78404487-78405040	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:78404855-78404972	K562	blood:	n/a	n/a
5	NFATC1	chr1:78404283-78405351	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:78403176-78414550	K562	blood:	n/a	n/a
7	POLR2A	chr1:78404321-78405503	GM12878	blood:	n/a	n/a
8	MTA3	chr1:78404325-78405581	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:78404378-78405162	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:78404744-78405572	HL-60	blood:	n/a	n/a
11	POLR2A	chr1:78404679-78405441	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:78404345-78406094	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:78404711-78405477	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:78404355-78405285	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:78403523-78409142	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:78404218-78405528	HCT-116	colon:	n/a	n/a
17	POLR2A	chr1:78404704-78405434	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:78404475-78406191	A549	lung:	n/a	n/a
19	POLR2A	chr1:78404407-78405409	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:78404661-78405891	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:78404872-78405221	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:78404245-78405176	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr1:78404931-78405171	U87	brain:	n/a	n/a
24	POLR2A	chr1:78404887-78405150	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr1:78404216-78408732	GM12891	blood:	n/a	n/a
26	POLR2A	chr1:78404279-78406092	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:78404868-78405078	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:78402316-78405990	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr1:78404088-78409674	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr1:78404341-78405286	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:78404195-78404991	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr1:78404324-78404965	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:78404336-78405500	GM12891	blood:	n/a	n/a
34	BCL3	chr1:78404834-78405566	A549	lung:	n/a	n/a
35	POLR2A	chr1:78404780-78405514	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr1:78404369-78405874	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr1:78404699-78405150	IMR90	lung:	n/a	n/a
38	POLR2A	chr1:78404820-78404961	H1-hESC	embryonic stem cell:	n/a	n/a
39	NFATC1	chr1:78404191-78407972	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:78404692-78405349	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78402015..78405926-chr1:78406152..78409189,6	K562	blood:
2	chr1:78399819..78401353-chr1:78403324..78406148,2	K562	blood:
3	chr1:78395727..78397922-chr1:78404779..78406771,2	K562	blood:

No data

Variant related genes	Relation type
NEXN	TF binding region
ENSG00000162614	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12409081	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1749912	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1984298	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs599987	1.00[ASN][1000 genomes]
rs6424666	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs661038	0.81[MEX][hapmap]
rs6656888	0.82[MEX][hapmap]
rs7531525	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78356200-78408600	Weak transcription	HMEC	breast
2	chr1:78367000-78407000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:78371600-78413000	Weak transcription	Psoas Muscle	Psoas
4	chr1:78372800-78418600	Weak transcription	Pancreas	Pancrea
5	chr1:78382200-78407400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:78382200-78408000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:78382400-78405600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:78383600-78418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:78384600-78406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:78387800-78412600	Weak transcription	Fetal Brain Male	brain
11	chr1:78388600-78416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:78388800-78410000	Strong transcription	HSMMtube	muscle
13	chr1:78389000-78414600	Strong transcription	NH-A	brain
14	chr1:78390200-78409800	Weak transcription	NHEK	skin
15	chr1:78391200-78407000	Weak transcription	Fetal Kidney	kidney
16	chr1:78391200-78407200	Strong transcription	Osteobl	bone
17	chr1:78392000-78406200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:78392000-78411000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:78392200-78420400	Strong transcription	HSMM	muscle
20	chr1:78392800-78405000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:78392800-78408800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:78393000-78405800	Weak transcription	Fetal Thymus	thymus
23	chr1:78393000-78406800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:78393000-78418600	Weak transcription	Lung	lung
25	chr1:78393200-78408000	Weak transcription	Primary B cells from cord blood	blood
26	chr1:78393200-78417400	Weak transcription	Small Intestine	intestine
27	chr1:78393400-78409000	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:78393400-78418000	Weak transcription	Stomach Mucosa	stomach
29	chr1:78394000-78406600	Weak transcription	GM12878-XiMat	blood
30	chr1:78394000-78407600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:78394000-78411400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:78394200-78406400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:78396200-78406600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:78396200-78414400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr1:78396400-78407800	Weak transcription	Placenta	Placenta
36	chr1:78396800-78405000	Weak transcription	Fetal Heart	heart
37	chr1:78396800-78411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:78396800-78415800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:78396800-78419600	Weak transcription	Ovary	ovary
40	chr1:78397400-78406000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:78397400-78406600	Weak transcription	Adipose Nuclei	Adipose
42	chr1:78397800-78418600	Weak transcription	Spleen	Spleen
43	chr1:78398200-78405400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:78398600-78418400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:78399000-78408200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr1:78399600-78407200	Strong transcription	Left Ventricle	heart
47	chr1:78400000-78405600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:78400200-78407400	Weak transcription	NHDF-Ad	bronchial
49	chr1:78400400-78407000	Weak transcription	Dnd41	blood
50	chr1:78400400-78417200	Weak transcription	Gastric	stomach

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