Variant report

Variant	rs6982197
Chromosome Location	chr8:125549726-125549727
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:125549583-125551914	GM12891	blood:	n/a	n/a
2	MXI1	chr8:125549508-125552974	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr8:125549444-125552363	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr8:125549416-125551632	K562	blood:	n/a	n/a
5	POLR2A	chr8:125549084-125552483	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125547667..125554911-chr8:125566055..125572382,17	MCF-7	breast:
2	chr8:125548205..125551096-chr8:125575812..125578141,2	MCF-7	breast:
3	chr8:125549492..125551989-chr8:125824960..125829256,5	K562	blood:
4	chr8:125547520..125551844-chr8:126101419..126105683,3	MCF-7	breast:
5	chr8:125548510..125551607-chr8:125929970..125932882,3	MCF-7	breast:
6	chr8:125515035..125519543-chr8:125547357..125551225,5	MCF-7	breast:
7	chr8:125461480..125466921-chr8:125547850..125552862,10	MCF-7	breast:
8	chr8:125461877..125466400-chr8:125548792..125551961,4	MCF-7	breast:
9	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
10	chr8:125491802..125498170-chr8:125548148..125552034,10	MCF-7	breast:
11	chr8:125548946..125551897-chr8:126103590..126105323,2	MCF-7	breast:
12	chr8:125484298..125489708-chr8:125549185..125553061,9	MCF-7	breast:
13	chr8:125483604..125491110-chr8:125548591..125554086,23	K562	blood:
14	chr8:125549374..125552995-chr8:126009841..126015179,7	MCF-7	breast:
15	chr8:125494945..125497543-chr8:125548660..125551608,2	K562	blood:
16	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
17	chr8:125548570..125552806-chr8:125825742..125828762,4	K562	blood:
18	chr8:125548069..125549733-chr9:130212828..130214669,2	MCF-7	breast:
19	chr8:125484053..125491713-chr8:125548138..125554442,21	K562	blood:
20	chr8:125548441..125550525-chr8:126045562..126047599,2	K562	blood:

No data

Variant related genes	Relation type
NDUFB9	TF binding region
ENSG00000164961	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000156831	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000250428	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000148356	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000104549	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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10092569	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10106292	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11991829	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12542293	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12548235	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28725399	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812471	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812472	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3812474	0.89[EUR][1000 genomes]
rs3812475	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[EUR][1000 genomes]
rs3886003	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4128468	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4269525	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]
rs4269526	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4870901	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4871498	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]
rs4871499	0.81[EUR][1000 genomes]
rs6470245	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6984985	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6987343	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6993926	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7001480	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7005393	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7007115	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7009290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7010411	0.90[JPT][hapmap]
rs7013683	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7812331	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7812911	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7825599	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7827791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7830506	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.84[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
rs6982197	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs6982197	TRMT12	cis	multi-tissue	Pritchard
rs6982197	TRMT12	cis	lymphoblastoid	seeQTL
rs6982197	TRMT12	cis	Whole Blood	GTEx
rs6982197	ZHX2	cis	parietal	SCAN

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	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
4	chr8:125519200-125550000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:125520000-125550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:125527600-125550200	Weak transcription	Fetal Brain Female	brain
7	chr8:125528000-125550400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:125531400-125550000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:125531600-125550000	Weak transcription	Fetal Lung	lung
10	chr8:125535800-125550000	Weak transcription	Thymus	Thymus
11	chr8:125537200-125550400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:125537800-125550400	Weak transcription	Esophagus	oesophagus
13	chr8:125538400-125549800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr8:125539400-125549800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:125539800-125550200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:125540000-125550000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr8:125540200-125549800	Weak transcription	NHDF-Ad	bronchial
18	chr8:125540200-125550000	Weak transcription	NH-A	brain
19	chr8:125540200-125550200	Weak transcription	Fetal Kidney	kidney
20	chr8:125540200-125550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr8:125541800-125550400	Weak transcription	Lung	lung
22	chr8:125543800-125550000	Weak transcription	Stomach Mucosa	stomach
23	chr8:125544000-125549800	Weak transcription	Fetal Heart	heart
24	chr8:125544000-125550000	Weak transcription	Colon Smooth Muscle	Colon
25	chr8:125544200-125550400	Weak transcription	Colonic Mucosa	Colon
26	chr8:125544400-125549800	Weak transcription	Brain Anterior Caudate	brain
27	chr8:125544400-125549800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr8:125544400-125549800	Weak transcription	Brain Substantia Nigra	brain
29	chr8:125544400-125550000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr8:125544400-125550000	Weak transcription	Right Ventricle	heart
31	chr8:125544400-125550200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr8:125544400-125550400	Weak transcription	Aorta	Aorta
33	chr8:125544600-125550400	Weak transcription	Left Ventricle	heart
34	chr8:125545000-125550000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr8:125545400-125550400	Weak transcription	Placenta	Placenta
36	chr8:125545800-125550000	Weak transcription	Fetal Muscle Leg	muscle
37	chr8:125545800-125550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:125545800-125550400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr8:125546000-125549800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr8:125546000-125550000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr8:125546000-125550000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr8:125546000-125550200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr8:125546000-125550200	Weak transcription	Fetal Thymus	thymus
44	chr8:125546000-125550400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr8:125546000-125550400	Weak transcription	Ovary	ovary
46	chr8:125546200-125550000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr8:125546200-125550000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr8:125546200-125550000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr8:125546200-125550200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr8:125546200-125550400	Weak transcription	Fetal Muscle Trunk	muscle

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