Variant report

Variant	rs2722195
Chromosome Location	chr12:104354290-104354291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 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	TAL1	chr12:104354265-104354903	K562	blood:	n/a	n/a
4	CREB1	chr12:104354163-104355017	K562	blood:	n/a	n/a
5	NR2F2	chr12:104354260-104354981	K562	blood:	n/a	n/a
6	POLR2A	chr12:104354017-104354327	U87	brain:	n/a	n/a
7	JUN	chr12:104354237-104355089	K562	blood:	n/a	n/a
8	NR2F2	chr12:104354193-104355140	K562	blood:	n/a	n/a
9	POLR2A	chr12:104353647-104354292	HepG2	liver:	n/a	n/a
10	TRIM28	chr12:104354224-104354946	K562	blood:	n/a	n/a
11	TEAD4	chr12:104354246-104354858	K562	blood:	n/a	n/a
12	POLR2A	chr12:104354017-104354479	U87	brain:	n/a	n/a
13	TEAD4	chr12:104354280-104354906	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
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]
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]
rs812498	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]

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
rs2722195	CHST11	cis	parietal	SCAN
rs2722195	C12orf73	cis	Artery Tibial	GTEx
rs2722195	MYBPC1	cis	cerebellum	SCAN
rs2722195	C12orf73	cis	Artery Aorta	GTEx

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	chr12:104351600-104354400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:104351600-104355600	Weak transcription	Brain Germinal Matrix	brain
5	chr12:104351600-104356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:104351600-104356400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:104351600-104356400	Weak transcription	Brain Angular Gyrus	brain
8	chr12:104351600-104357000	Weak transcription	Fetal Brain Female	brain
9	chr12:104351600-104357200	Weak transcription	GM12878-XiMat	blood
10	chr12:104351600-104357400	Weak transcription	Fetal Lung	lung
11	chr12:104351600-104357400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:104351600-104357600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:104351600-104357600	Weak transcription	NHLF	lung
14	chr12:104351600-104357800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:104351600-104357800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:104351600-104357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:104351600-104357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:104351600-104357800	Weak transcription	HSMMtube	muscle
19	chr12:104351600-104357800	Weak transcription	NHDF-Ad	bronchial
20	chr12:104351600-104357800	Weak transcription	NHEK	skin
21	chr12:104351600-104357800	Weak transcription	Osteobl	bone
22	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
28	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
29	chr12:104351600-104358000	Weak transcription	Ovary	ovary
30	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
32	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
33	chr12:104351600-104358000	Weak transcription	HMEC	breast
34	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
41	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
42	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
44	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:104352000-104355600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:104352000-104356200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:104352000-104357600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:104352000-104357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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