Variant report

Variant	rs4269525
Chromosome Location	chr8:125547654-125547655
allele	C/T
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	POLR2A	chr8:125547530-125547918	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr8:125546592-125548413	K562	blood:	n/a	n/a
3	CEBPB	chr8:125547411-125547674	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125487117..125490518-chr8:125542261..125547751,5	K562	blood:
2	chr8:125547520..125551844-chr8:126101419..126105683,3	MCF-7	breast:
3	chr8:125515035..125519543-chr8:125547357..125551225,5	MCF-7	breast:
4	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:

Variant related genes	Relation type
NDUFB9	TF binding region
ENSG00000170881	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000156831	Chromatin interaction
ENSG00000164961	Chromatin interaction
ENSG00000245149	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10091243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10092569	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10106292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11991829	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12542293	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12548235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28725399	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812471	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812472	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3812474	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3812475	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3886003	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4128468	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4269526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870901	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4871498	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871499	0.80[EUR][1000 genomes]
rs6470245	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6982197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6984985	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6987343	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6993926	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7001480	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7005393	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7007115	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7009290	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7010411	0.90[JPT][hapmap]
rs7013683	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7812331	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7812911	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7825599	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7827791	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7830506	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4269525	TRMT12	cis	lymphoblastoid	seeQTL
rs4269525	TRMT12	cis	Whole Blood	GTEx
rs4269525	TRMT12	cis	multi-tissue	Pritchard
rs4269525	ZHX2	cis	parietal	SCAN
rs4269525	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
4	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
6	chr8:125516200-125549600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr8:125516200-125549600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr8:125516400-125549600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr8:125519200-125550000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr8:125520000-125550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr8:125525200-125549600	Weak transcription	Brain Germinal Matrix	brain
12	chr8:125527600-125550200	Weak transcription	Fetal Brain Female	brain
13	chr8:125528000-125550400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr8:125531400-125550000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr8:125531600-125548400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr8:125531600-125550000	Weak transcription	Fetal Lung	lung
17	chr8:125535800-125550000	Weak transcription	Thymus	Thymus
18	chr8:125537200-125550400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr8:125537800-125550400	Weak transcription	Esophagus	oesophagus
20	chr8:125538200-125549600	Weak transcription	HUVEC	blood vessel
21	chr8:125538400-125549800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr8:125539000-125549400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr8:125539400-125549800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr8:125539600-125549600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:125539800-125549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr8:125539800-125550200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:125540000-125550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr8:125540200-125549400	Weak transcription	HMEC	breast
29	chr8:125540200-125549600	Weak transcription	HSMMtube	muscle
30	chr8:125540200-125549600	Weak transcription	Osteobl	bone
31	chr8:125540200-125549800	Weak transcription	NHDF-Ad	bronchial
32	chr8:125540200-125550000	Weak transcription	NH-A	brain
33	chr8:125540200-125550200	Weak transcription	Fetal Kidney	kidney
34	chr8:125540200-125550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:125541200-125548800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:125541400-125549000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:125541800-125548000	Weak transcription	HepG2	liver
38	chr8:125541800-125550400	Weak transcription	Lung	lung
39	chr8:125542000-125548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:125542800-125548400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr8:125542800-125548800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr8:125543800-125549600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:125543800-125549600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr8:125543800-125550000	Weak transcription	Stomach Mucosa	stomach
45	chr8:125544000-125549200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:125544000-125549400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr8:125544000-125549600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr8:125544000-125549800	Weak transcription	Fetal Heart	heart
49	chr8:125544000-125550000	Weak transcription	Colon Smooth Muscle	Colon
50	chr8:125544200-125549400	Weak transcription	Muscle Satellite Cultured Cells	--

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