Variant report

Variant	rs16899688
Chromosome Location	chr8:125569380-125569381
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:125568538-125569448	MCF-7	breast:	n/a	chr8:125568887-125568905 chr8:125568890-125568899 chr8:125568889-125568910 chr8:125568892-125568902 chr8:125568890-125568903
2	POLR2A	chr8:125569316-125569698	K562	blood:	n/a	n/a
3	POLR2A	chr8:125567717-125570111	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125547667..125554911-chr8:125566055..125572382,17	MCF-7	breast:
3	chr8:125569223..125571926-chr8:125574045..125576529,2	K562	blood:
4	chr5:176852795..176855032-chr8:125568012..125570778,2	MCF-7	breast:
5	chr8:125567601..125570100-chr8:125573465..125576752,3	MCF-7	breast:
6	chr8:125550901..125553938-chr8:125568241..125570881,3	K562	blood:
7	chr8:125550147..125552790-chr8:125567789..125570449,2	MCF-7	breast:

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000198055	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000147684	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10094916	0.88[CEU][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap]
rs10099056	0.85[CEU][hapmap]
rs10103773	0.85[CEU][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap]
rs10110655	0.85[CEU][hapmap];0.83[YRI][hapmap]
rs11778396	0.91[YRI][hapmap]
rs11783209	0.85[CEU][hapmap]
rs13255599	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs2303955	0.85[CEU][hapmap]
rs3763542	0.85[CEU][hapmap]
rs3829035	0.83[YRI][hapmap]
rs4489311	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs6470253	0.85[CEU][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap]
rs6470254	0.85[CEU][hapmap];0.91[YRI][hapmap]
rs7010757	0.85[LWK][hapmap];0.91[YRI][hapmap]
rs7015228	0.85[CEU][hapmap]
rs7015374	0.85[CEU][hapmap];0.91[YRI][hapmap]
rs7835397	0.83[YRI][hapmap]
rs7841224	0.92[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][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	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv465801	chr8:125565328-125576681	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv612145	chr8:125565328-125576681	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16899688	TRMT12	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
3	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
5	chr8:125554000-125572400	Strong transcription	Thymus	Thymus
6	chr8:125554000-125574000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr8:125554200-125570000	Strong transcription	Fetal Thymus	thymus
8	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:125554400-125574200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr8:125554400-125575400	Strong transcription	Primary B cells from cord blood	blood
11	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
12	chr8:125554600-125574000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:125554600-125575000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr8:125554600-125575800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr8:125555200-125574000	Strong transcription	Placenta	Placenta
16	chr8:125555200-125575000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr8:125555200-125575200	Strong transcription	Brain Cingulate Gyrus	brain
18	chr8:125555600-125574200	Strong transcription	Primary T cells from cord blood	blood
19	chr8:125556000-125574200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr8:125556200-125575000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr8:125556800-125576800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr8:125557000-125572400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:125558000-125575600	Weak transcription	Stomach Mucosa	stomach
24	chr8:125558200-125573600	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr8:125558800-125573200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr8:125559000-125572600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr8:125559200-125572400	Strong transcription	Lung	lung
28	chr8:125560400-125575000	Weak transcription	Right Atrium	heart
29	chr8:125561200-125572800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr8:125561200-125575200	Strong transcription	HepG2	liver
31	chr8:125561400-125572400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr8:125561400-125575000	Strong transcription	Adipose Nuclei	Adipose
33	chr8:125561400-125575600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:125561600-125571800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr8:125561600-125573400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:125561600-125575000	Strong transcription	Liver	Liver
37	chr8:125563400-125572600	Strong transcription	Spleen	Spleen
38	chr8:125563600-125569400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:125563600-125574400	Strong transcription	Right Ventricle	heart
40	chr8:125563600-125575600	Strong transcription	Fetal Stomach	stomach
41	chr8:125564000-125574000	Weak transcription	K562	blood
42	chr8:125564000-125574200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr8:125564000-125575600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr8:125564200-125572600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:125564200-125574000	Strong transcription	Brain Germinal Matrix	brain
46	chr8:125564400-125572400	Strong transcription	Esophagus	oesophagus
47	chr8:125564400-125572800	Weak transcription	HSMMtube	muscle
48	chr8:125564400-125576800	Strong transcription	Fetal Intestine Small	intestine
49	chr8:125564800-125573400	Weak transcription	Hela-S3	cervix
50	chr8:125565600-125572400	Strong transcription	Pancreas	Pancrea

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