Variant report

Variant	rs172814
Chromosome Location	chr12:104357814-104357815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104357713-104358480	K562	blood:	n/a	n/a
2	POLR2A	chr12:104357794-104360395	SK-N-MC	brain:	n/a	n/a
3	ZNF384	chr12:104357697-104358081	K562	blood:	n/a	n/a
4	ZNF384	chr12:104357709-104358024	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:104357812-104358281	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:104357686-104357916	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104356512..104358461-chr12:104416021..104418355,2	K562	blood:
2	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:
3	chr12:104357292..104359018-chr12:104494120..104496296,2	MCF-7	breast:
4	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
5	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
6	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:
7	chr12:104324052..104326463-chr12:104355875..104358112,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDG-1	chr12:104357017-104357920	NONHSAT030400
2	lnc-C12orf73-2	chr12:104357568-104359481	NONHSAT030401

No data

Variant related genes	Relation type
TDG	TF binding region
ENSG00000166598	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1177458	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2254063	0.82[EUR][1000 genomes]
rs2254064	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2576973	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2583227	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583251	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583260	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583261	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2583263	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583277	0.83[EUR][1000 genomes]
rs2629768	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2629770	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2629771	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2629779	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2700510	0.91[AFR][1000 genomes]
rs2722200	0.91[AFR][1000 genomes]
rs2723846	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723847	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723876	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs322102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs322105	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322107	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322108	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs322110	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs784081	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs796736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs172814	KRTHB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 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	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
9	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
10	chr12:104351600-104358000	Weak transcription	Ovary	ovary
11	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
13	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
14	chr12:104351600-104358000	Weak transcription	HMEC	breast
15	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
22	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
23	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
25	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:104352000-104358000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:104352000-104358000	Weak transcription	Left Ventricle	heart
30	chr12:104352000-104358400	Weak transcription	Primary B cells from cord blood	blood
31	chr12:104352200-104358200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:104352600-104358000	Weak transcription	Liver	Liver
33	chr12:104352600-104358000	Weak transcription	HUVEC	blood vessel
34	chr12:104353000-104358200	Weak transcription	Hela-S3	cervix
35	chr12:104354200-104358000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:104354600-104358000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:104355200-104358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:104355600-104358000	Enhancers	Brain Germinal Matrix	brain
39	chr12:104355600-104358000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:104356600-104358000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:104356600-104358000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:104356600-104358200	Enhancers	HepG2	liver
43	chr12:104357000-104358400	Enhancers	Brain Angular Gyrus	brain
44	chr12:104357200-104358000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:104357200-104358000	Enhancers	GM12878-XiMat	blood
46	chr12:104357200-104358200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:104357200-104358200	Weak transcription	Fetal Brain Female	brain
48	chr12:104357400-104358000	Enhancers	Stomach Smooth Muscle	stomach
49	chr12:104357400-104358200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr12:104357400-104358400	Enhancers	Fetal Lung	lung

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