Variant report

Variant	rs12374446
Chromosome Location	chr5:179131143-179131144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179131030-179131910	K562	blood:	n/a	n/a
2	POLR2A	chr5:179130952-179131147	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:179130980-179131162	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr5:179131138-179131178	K562	blood:	n/a	n/a
5	POLR2A	chr5:179130415-179131249	K562	blood:	n/a	n/a
6	POLR2A	chr5:179130131-179131822	GM12892	blood:	n/a	n/a
7	POLR2A	chr5:179130630-179131589	K562	blood:	n/a	n/a
8	POLR2A	chr5:179130323-179133333	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr5:179130591-179131313	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr5:179130375-179131291	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:179130719-179131281	GM12892	blood:	n/a	n/a
12	POLR2A	chr5:179130813-179131195	GM12891	blood:	n/a	n/a
13	POLR2A	chr5:179130788-179131820	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:179130785-179131561	GM12891	blood:	n/a	n/a
15	POLR2A	chr5:179130447-179131259	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr5:179130660-179131227	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr5:179130801-179131233	GM12891	blood:	n/a	n/a
18	POLR2A	chr5:179130694-179131322	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179127758..179131964-chr5:179232228..179234815,3	MCF-7	breast:
2	chr5:179130758..179132404-chr5:179133723..179135706,3	MCF-7	breast:
3	chr5:179130512..179134437-chr5:179159497..179161438,3	MCF-7	breast:
4	chr5:179102777..179105502-chr5:179129566..179131277,2	MCF-7	breast:
5	chr5:179130815..179133473-chr5:179133659..179136452,3	MCF-7	breast:
6	chr5:179129685..179132691-chr5:179151182..179153644,5	K562	blood:
7	chr5:179128478..179132558-chr5:179135787..179140840,4	MCF-7	breast:
8	chr5:179123586..179129079-chr5:179129217..179136579,19	MCF-7	breast:
9	chr5:179129372..179132984-chr5:179141701..179145363,3	K562	blood:

No data

Variant related genes	Relation type
CANX	TF binding region
ENSG00000161011	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000161021	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1019443	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap]
rs10447303	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10447304	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10516146	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10794700	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10903245	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12374485	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522926	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs12652934	0.81[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs13172893	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13174472	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13182141	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13184690	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34329357	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34646062	0.92[ASW][hapmap];0.85[CEU][hapmap]
rs34785307	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35320050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797774	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56227602	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56807514	0.91[EUR][1000 genomes]
rs62404348	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62406180	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7444571	0.83[ASN][1000 genomes]
rs7732112	0.82[AFR][1000 genomes]
rs7736300	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12374446	CANX	cis	parietal	SCAN
rs12374446	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs12374446	CANX	cis	cerebellum	SCAN
rs12374446	C5orf45	cis	cerebellum	SCAN
rs12374446	MAML1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179127200-179132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:179127400-179137800	Weak transcription	Aorta	Aorta
3	chr5:179127600-179132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:179127800-179131800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:179127800-179132000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:179127800-179132200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:179127800-179132200	Weak transcription	NH-A	brain
8	chr5:179127800-179132600	Weak transcription	Primary T cells from cord blood	blood
9	chr5:179127800-179133200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:179127800-179133200	Weak transcription	Brain Anterior Caudate	brain
11	chr5:179127800-179133200	Weak transcription	Fetal Brain Female	brain
12	chr5:179127800-179133400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:179127800-179133600	Weak transcription	Brain Angular Gyrus	brain
14	chr5:179127800-179133600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:179127800-179133600	Weak transcription	Brain Substantia Nigra	brain
16	chr5:179127800-179133600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:179127800-179133800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:179127800-179133800	Weak transcription	Colonic Mucosa	Colon
19	chr5:179127800-179134000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:179127800-179134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:179127800-179136000	Weak transcription	HSMMtube	muscle
22	chr5:179127800-179152000	Strong transcription	NHEK	skin
23	chr5:179127800-179156400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:179127800-179156600	Strong transcription	Fetal Stomach	stomach
25	chr5:179127800-179158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:179128000-179132400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:179128000-179135000	Weak transcription	Esophagus	oesophagus
28	chr5:179128200-179131800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:179128200-179156400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:179128400-179132400	Weak transcription	HMEC	breast
31	chr5:179128400-179132800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:179128400-179133200	Weak transcription	Gastric	stomach
33	chr5:179128400-179143200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:179128400-179157800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:179128400-179157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:179128400-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:179128400-179159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:179128600-179131200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:179128600-179132600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:179128600-179133200	Weak transcription	Primary B cells from cord blood	blood
41	chr5:179128600-179133600	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:179128600-179150400	Weak transcription	Stomach Mucosa	stomach
43	chr5:179128600-179158200	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:179128800-179131200	Genic enhancers	K562	blood
45	chr5:179128800-179131400	Strong transcription	A549	lung
46	chr5:179129000-179131200	Strong transcription	Brain Germinal Matrix	brain
47	chr5:179129000-179158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:179129200-179132000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:179129200-179132400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:179129200-179133200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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