Variant report

Variant	rs4871498
Chromosome Location	chr8:125538754-125538755
allele	C/G
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	chr8:125537849-125541960	K562	blood:	n/a	n/a
2	NR2F2	chr8:125538056-125539697	MCF-7	breast:	n/a	n/a
3	CTCF	chr8:125537923-125538766	A549	lung:	n/a	n/a
4	NFATC1	chr8:125538709-125540511	GM12878	blood:	n/a	n/a
5	ZNF143	chr8:125538176-125539182	GM12878	blood:	n/a	chr8:125538995-125539004
6	FOXM1	chr8:125538110-125538794	ECC-1	luminal epithelium:	n/a	n/a
7	PML	chr8:125538741-125540525	GM12878	blood:	n/a	n/a
8	ARID3A	chr8:125538058-125538850	K562	blood:	n/a	n/a
9	MTA3	chr8:125538745-125540528	GM12878	blood:	n/a	n/a
10	RUNX3	chr8:125538644-125540478	GM12878	blood:	n/a	chr8:125538993-125539002 chr8:125538993-125539002
11	POLR2A	chr8:125538201-125540393	GM12878	blood:	n/a	n/a
12	GATA3	chr8:125538080-125539486	MCF-7	breast:	n/a	chr8:125538117-125538127 chr8:125538120-125538127 chr8:125538116-125538132 chr8:125538113-125538134 chr8:125538120-125538127 chr8:125538722-125538735 chr8:125538116-125538132 chr8:125538120-125538127
13	POLR2A	chr8:125538060-125539113	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr8:125538549-125539255	MCF-7	breast:	n/a	chr8:125538722-125538735
15	EP300	chr8:125538590-125539148	GM12878	blood:	n/a	n/a
16	RUNX3	chr8:125538130-125540496	GM12878	blood:	n/a	chr8:125538993-125539002 chr8:125538993-125539002
17	CTCF	chr8:125538640-125538790	AG10803	skin:	n/a	n/a
18	POLR2A	chr8:125538226-125538853	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125476818..125478783-chr8:125536249..125538761,2	MCF-7	breast:
2	chr8:125503534..125506808-chr8:125536853..125540308,3	MCF-7	breast:
3	chr8:125530085..125533438-chr8:125536669..125540173,3	K562	blood:
4	chr8:125458668..125465446-chr8:125536808..125541745,7	MCF-7	breast:
5	chr8:125485755..125491202-chr8:125535208..125540184,8	MCF-7	breast:
6	chr8:125484651..125489587-chr8:125535041..125543731,11	K562	blood:
7	chr8:125485366..125490256-chr8:125538202..125541512,6	K562	blood:
8	chr8:125504585..125506725-chr8:125538257..125539787,2	K562	blood:
9	chr8:125520162..125523153-chr8:125538508..125540533,2	MCF-7	breast:
10	chr8:125469347..125472316-chr8:125538366..125541222,2	K562	blood:
11	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
12	chr8:125538432..125540496-chr8:125866571..125869379,2	MCF-7	breast:

Variant related genes	Relation type
TATDN1	TF binding region
ENSG00000245149	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000170881	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10091243	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10092569	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10106292	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11987932	0.82[EUR][1000 genomes]
rs11991829	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12542293	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12548235	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28725399	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3812474	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3812475	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3886003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4128468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4269525	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]
rs4269526	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6470245	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6982197	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6984985	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6987343	0.92[CEU][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6993926	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7001480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005393	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7007115	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7009290	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7010411	0.91[JPT][hapmap]
rs7013683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7812331	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7812911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7825599	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7827791	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7830506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4871498	TRMT12	cis	uninvolved skin	skin_eQTL
rs4871498	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs4871498	TRMT12	cis	Whole Blood	GTEx

Chromatin state (count:126 , 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	chr8:125489000-125541200	Weak transcription	Gastric	stomach
3	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
4	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
8	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
10	chr8:125516200-125543600	Weak transcription	Aorta	Aorta
11	chr8:125516200-125549600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr8:125516200-125549600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr8:125516400-125549600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr8:125519200-125550000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:125520000-125550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr8:125525200-125549600	Weak transcription	Brain Germinal Matrix	brain
17	chr8:125526600-125541000	Weak transcription	Colonic Mucosa	Colon
18	chr8:125527200-125539600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:125527400-125541000	Weak transcription	Fetal Heart	heart
20	chr8:125527600-125550200	Weak transcription	Fetal Brain Female	brain
21	chr8:125528000-125550400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr8:125529200-125539600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr8:125529200-125543600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:125529200-125544000	Weak transcription	Fetal Stomach	stomach
25	chr8:125529400-125539600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr8:125529400-125543200	Weak transcription	Fetal Muscle Leg	muscle
27	chr8:125531400-125541200	Weak transcription	Hela-S3	cervix
28	chr8:125531400-125542600	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:125531400-125547400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr8:125531400-125550000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:125531600-125543400	Weak transcription	Fetal Thymus	thymus
32	chr8:125531600-125543600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr8:125531600-125544200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr8:125531600-125548400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:125531600-125550000	Weak transcription	Fetal Lung	lung
36	chr8:125531800-125541200	Weak transcription	Left Ventricle	heart
37	chr8:125532000-125543000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:125532000-125544000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr8:125532200-125540600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr8:125532200-125543400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr8:125532200-125543800	Weak transcription	Placenta	Placenta
42	chr8:125532200-125544000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr8:125534000-125542600	Weak transcription	Dnd41	blood
44	chr8:125535000-125539000	Enhancers	Brain Cingulate Gyrus	brain
45	chr8:125535400-125538800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:125535400-125539400	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr8:125535400-125540000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr8:125535600-125538800	Enhancers	Adipose Nuclei	Adipose
49	chr8:125535600-125539600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr8:125535600-125543400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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