Variant report

Variant	rs812498
Chromosome Location	chr12:104354799-104354800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104354215-104355425	K562	blood:	n/a	n/a
2	POLR2A	chr12:104354261-104354823	MCF10A-Er-Src	breast:	n/a	n/a
3	EGR1	chr12:104354636-104354934	K562	blood:	n/a	n/a
4	TAL1	chr12:104354265-104354903	K562	blood:	n/a	n/a
5	POLR2A	chr12:104354691-104354961	K562	blood:	n/a	n/a
6	CREB1	chr12:104354163-104355017	K562	blood:	n/a	n/a
7	NR2F2	chr12:104354260-104354981	K562	blood:	n/a	n/a
8	MAX	chr12:104354370-104354930	K562	blood:	n/a	n/a
9	ATF1	chr12:104354346-104354961	K562	blood:	n/a	n/a
10	JUND	chr12:104354319-104354917	K562	blood:	n/a	n/a
11	JUN	chr12:104354237-104355089	K562	blood:	n/a	n/a
12	MAX	chr12:104354372-104354894	K562	blood:	n/a	n/a
13	NR2F2	chr12:104354193-104355140	K562	blood:	n/a	n/a
14	MYC	chr12:104354325-104354853	K562	blood:	n/a	n/a
15	SIN3AK20	chr12:104354359-104354866	K562	blood:	n/a	n/a
16	RCOR1	chr12:104354794-104354866	K562	blood:	n/a	n/a
17	TRIM28	chr12:104354224-104354946	K562	blood:	n/a	n/a
18	TEAD4	chr12:104354246-104354858	K562	blood:	n/a	n/a
19	CBX3	chr12:104354302-104354884	K562	blood:	n/a	n/a
20	TEAD4	chr12:104354280-104354906	K562	blood:	n/a	n/a
21	EP300	chr12:104354311-104354892	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:

No data

Variant related genes	Relation type
C12orf73	TF binding region
TDG	TF binding region
ENSG00000166598	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000265072	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17034968	1.00[ASN][1000 genomes]
rs17034974	1.00[ASN][1000 genomes]
rs17035120	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs2249210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293621	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2583259	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2722193	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763995	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.99[ASN][1000 genomes]
rs3763996	1.00[ASN][1000 genomes]
rs4135042	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4135067	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4135077	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4964142	1.00[ASN][1000 genomes]
rs4964163	0.97[ASN][1000 genomes]
rs4964164	0.96[ASN][1000 genomes]
rs73177938	1.00[ASN][1000 genomes]
rs73177942	1.00[ASN][1000 genomes]
rs73177950	0.97[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1799879	chr12:104351057-104360713	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs812498	MYBPC1	cis	cerebellum	SCAN
rs812498	C12orf73	cis	Artery Tibial	GTEx
rs812498	C12orf73	cis	Artery Aorta	GTEx
rs812498	CHST11	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104351400-104358000	Weak transcription	Lung	lung
2	chr12:104351400-104358000	Weak transcription	Spleen	Spleen
3	chr12:104351600-104355600	Weak transcription	Brain Germinal Matrix	brain
4	chr12:104351600-104356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:104351600-104356400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:104351600-104356400	Weak transcription	Brain Angular Gyrus	brain
7	chr12:104351600-104357000	Weak transcription	Fetal Brain Female	brain
8	chr12:104351600-104357200	Weak transcription	GM12878-XiMat	blood
9	chr12:104351600-104357400	Weak transcription	Fetal Lung	lung
10	chr12:104351600-104357400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:104351600-104357600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:104351600-104357600	Weak transcription	NHLF	lung
13	chr12:104351600-104357800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:104351600-104357800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:104351600-104357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:104351600-104357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:104351600-104357800	Weak transcription	HSMMtube	muscle
18	chr12:104351600-104357800	Weak transcription	NHDF-Ad	bronchial
19	chr12:104351600-104357800	Weak transcription	NHEK	skin
20	chr12:104351600-104357800	Weak transcription	Osteobl	bone
21	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
27	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
28	chr12:104351600-104358000	Weak transcription	Ovary	ovary
29	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
31	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
32	chr12:104351600-104358000	Weak transcription	HMEC	breast
33	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
40	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
43	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:104352000-104355600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:104352000-104356200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:104352000-104357600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:104352000-104357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:104352000-104357800	Weak transcription	Primary T cells fromperipheralblood	blood

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