Variant report

Variant	rs6993926
Chromosome Location	chr8:125501889-125501890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125495517..125498370-chr8:125499214..125502183,3	MCF-7	breast:
2	chr8:125501162..125503878-chr8:125549908..125551585,2	K562	blood:
3	chr4:80053807..80054491-chr8:125501594..125502544,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF139-1	chr8:125500751-125502523	ENSG00000253106.1

Variant related genes	Relation type
ENSG00000170881	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000147684	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10091243	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10092569	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10106292	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11987932	0.81[EUR][1000 genomes]
rs11991829	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12542293	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12548235	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28725399	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812471	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812472	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812474	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3812475	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3886003	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4128468	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4269525	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4269526	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4870901	0.83[AMR][1000 genomes]
rs4871498	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6470245	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6982197	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6984985	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6987343	0.89[EUR][1000 genomes]
rs7001480	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7005393	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7007115	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7009290	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7013683	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7812331	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7812911	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7825599	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827791	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7830506	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6993926	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs6993926	TRMT12	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488000-125503400	Weak transcription	Spleen	Spleen
2	chr8:125488200-125515800	Weak transcription	Lung	lung
3	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:125489000-125503400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:125489000-125505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:125489000-125519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:125489000-125531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:125489000-125541200	Weak transcription	Gastric	stomach
9	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
10	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr8:125496000-125512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:125496800-125503400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:125496800-125503400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr8:125496800-125513200	Weak transcription	Brain Angular Gyrus	brain
16	chr8:125496800-125521200	Weak transcription	Fetal Heart	heart
17	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr8:125497600-125505200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr8:125497800-125502400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr8:125497800-125504000	Strong transcription	Primary B cells from cord blood	blood
21	chr8:125497800-125506200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:125498000-125502600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:125498000-125502600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr8:125498000-125503600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr8:125498000-125503800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr8:125498000-125503800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr8:125498000-125504000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr8:125498000-125504000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr8:125498000-125504000	Strong transcription	Fetal Thymus	thymus
30	chr8:125498000-125504200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr8:125498000-125504400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr8:125498000-125504600	Strong transcription	Primary T cells from cord blood	blood
33	chr8:125498000-125504600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr8:125498000-125505000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr8:125498000-125505800	Strong transcription	Dnd41	blood
36	chr8:125498000-125506200	Strong transcription	Fetal Intestine Large	intestine
37	chr8:125498000-125506600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:125498000-125506800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr8:125498200-125502000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr8:125498200-125502200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr8:125498200-125502200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:125498200-125502400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr8:125498200-125502400	Strong transcription	Adipose Nuclei	Adipose
44	chr8:125498200-125502400	Strong transcription	HSMM	muscle
45	chr8:125498200-125502600	Strong transcription	HMEC	breast
46	chr8:125498200-125502800	Strong transcription	Liver	Liver
47	chr8:125498200-125503400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr8:125498200-125503800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:125498200-125503800	Strong transcription	Placenta	Placenta
50	chr8:125498200-125504000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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