Variant report

Variant	rs3812474
Chromosome Location	chr8:125463098-125463099
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:386)
CpG islands
(count:122)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:386 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr8:125462690-125463448	H1-hESC	embryonic stem cell:	n/a	n/a
2	IRF1	chr8:125462429-125463316	K562	blood:	n/a	n/a
3	GABPA	chr8:125462774-125463494	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr8:125462885-125463281	HUVEC	blood vessel:	n/a	n/a
5	ELK1	chr8:125462393-125463256	Hela-S3	cervix:	n/a	n/a
6	YY1	chr8:125462379-125463491	K562	blood:	n/a	chr8:125462971-125462981 chr8:125462970-125462978 chr8:125462972-125462980 chr8:125462959-125462981
7	SPI1	chr8:125463009-125463169	GM12878	blood:	n/a	n/a
8	POLR2A	chr8:125462442-125463882	GM12891	blood:	n/a	n/a
9	TAF1	chr8:125462427-125463343	PFSK-1	brain:	n/a	n/a
10	HDAC2	chr8:125462514-125463934	MCF-7	breast:	n/a	n/a
11	GABPA	chr8:125462602-125463274	Hela-S3	cervix:	n/a	n/a
12	YY1	chr8:125462884-125463156	K562	blood:	n/a	chr8:125462971-125462981 chr8:125462970-125462978 chr8:125462972-125462980 chr8:125462959-125462981
13	MAX	chr8:125462710-125463378	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr8:125462905-125463304	ECC-1	luminal epithelium:	n/a	n/a
15	CREB1	chr8:125462513-125463381	GM12878	blood:	n/a	n/a
16	SIX5	chr8:125462796-125463181	K562	blood:	n/a	n/a
17	CHD1	chr8:125462551-125463587	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr8:125462890-125463252	GM12891	blood:	n/a	n/a
19	REST	chr8:125462781-125463336	HL-60	blood:	n/a	chr8:125463079-125463092 chr8:125462848-125462868
20	ZNF384	chr8:125462445-125463261	GM12878	blood:	n/a	n/a
21	TAF1	chr8:125462839-125463248	Hela-S3	cervix:	n/a	n/a
22	ETS1	chr8:125462425-125463390	A549	lung:	n/a	n/a
23	ATF2	chr8:125462543-125463201	GM12878	blood:	n/a	n/a
24	TAF1	chr8:125462748-125463411	A549	lung:	n/a	n/a
25	EGR1	chr8:125462514-125463904	MCF-7	breast:	n/a	n/a
26	MAX	chr8:125462519-125463268	A549	lung:	n/a	n/a
27	POLR2A	chr8:125462440-125463414	Hela-S3	cervix:	n/a	n/a
28	FOXP2	chr8:125462811-125463246	SK-N-MC	brain:	n/a	n/a
29	SIN3AK20	chr8:125462907-125463368	PFSK-1	brain:	n/a	n/a
30	ELF1	chr8:125462772-125463321	SK-N-SH	brain:	n/a	chr8:125463059-125463072
31	POLR2A	chr8:125462428-125463291	GM18526	blood:	n/a	n/a
32	SPI1	chr8:125462934-125463222	GM12878	blood:	n/a	n/a
33	CTCF	chr8:125462389-125463102	GM12878	blood:	n/a	n/a
34	POLR2A	chr8:125462931-125463300	H1-hESC	embryonic stem cell:	n/a	n/a
35	SETDB1	chr8:125462697-125463261	U2OS	brain:	n/a	n/a
36	RUNX3	chr8:125462439-125463216	GM12878	blood:	n/a	n/a
37	THAP1	chr8:125462512-125463154	K562	blood:	n/a	chr8:125462956-125462980
38	CREB1	chr8:125462799-125463345	H1-hESC	embryonic stem cell:	n/a	n/a
39	BHLHE40	chr8:125462845-125463407	GM12878	blood:	n/a	n/a
40	YY1	chr8:125462512-125463324	ECC-1	luminal epithelium:	n/a	chr8:125462971-125462981 chr8:125462970-125462978 chr8:125462972-125462980 chr8:125462959-125462981
41	YY1	chr8:125462391-125463264	GM12878	blood:	n/a	chr8:125462971-125462981 chr8:125462970-125462978 chr8:125462972-125462980 chr8:125462959-125462981
42	MAX	chr8:125462785-125463341	H1-hESC	embryonic stem cell:	n/a	n/a
43	ELF1	chr8:125462814-125463235	A549	lung:	n/a	chr8:125463059-125463072
44	SIN3AK20	chr8:125462372-125463335	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr8:125462836-125463287	Hela-S3	cervix:	n/a	n/a
46	MYC	chr8:125462913-125463149	K562	blood:	n/a	n/a
47	BHLHE40	chr8:125462913-125463188	K562	blood:	n/a	n/a
48	USF2	chr8:125462436-125463212	Hela-S3	cervix:	n/a	n/a
49	NRF1	chr8:125462840-125463249	GM12878	blood:	n/a	n/a
50	POLR2A	chr8:125462920-125463337	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:125463066-125463116	NT2-D1	testis:	n/a
2	chr8:125463057-125463107	HCF	heart:	n/a
3	chr8:125463057-125463107	PFSK-1	brain:	n/a
4	chr8:125463066-125463116	NHDF-neo	bronchial:	n/a
5	chr8:125463057-125463107	MCF-7	breast:	n/a
6	chr8:125463066-125463116	HL-60	blood:	n/a
7	chr8:125463057-125463107	U87	brain:	n/a
8	chr8:125463057-125463107	HIPEpiC	eye:	n/a
9	chr8:125463057-125463107	HMEC	breast:	n/a
10	chr8:125463066-125463116	HNPCEpiC	eye:	n/a
11	chr8:125463066-125463116	PFSK-1	brain:	n/a
12	chr8:125463057-125463107	AG04450	lung:	fetal
13	chr8:125463057-125463107	HCPEpiC	choroid plexus:	n/a
14	chr8:125463066-125463116	GM12892	blood:	n/a
15	chr8:125463057-125463107	RPTEC	kidney:	n/a
16	chr8:125463066-125463116	K562	blood:	n/a
17	chr8:125463066-125463116	CMK	blood:	n/a
18	chr8:125463066-125463116	H1-hESC	embryonic stem cell:	embryo
19	chr8:125463057-125463107	PANC-1	pancreas:	n/a
20	chr8:125463066-125463116	BE2_C	brain:	n/a
21	chr8:125463057-125463107	HEEpiC	esophagus:	n/a
22	chr8:125463066-125463116	SKMC	muscle:	n/a
23	chr8:125463066-125463116	HAEpiC	amniotic membrane:	n/a
24	chr8:125463066-125463116	HepG2	liver:	n/a
25	chr8:125463057-125463107	BJ	skin:	n/a
26	chr8:125463057-125463107	HCM	heart:	n/a
27	chr8:125463057-125463107	Hela-S3	cervix:	n/a
28	chr8:125463057-125463107	HUVEC	blood vessel:	n/a
29	chr8:125463066-125463116	HMEC	breast:	n/a
30	chr8:125463057-125463107	CMK	blood:	n/a
31	chr8:125463057-125463107	HL-60	blood:	n/a
32	chr8:125463057-125463107	HCT-116	colon:	n/a
33	chr8:125463066-125463116	GM12878	blood:	n/a
34	chr8:125463066-125463116	GM06990	blood:	n/a
35	chr8:125463066-125463116	AG09309	skin:	n/a
36	chr8:125463066-125463116	U87	brain:	n/a
37	chr8:125463066-125463116	Hela-S3	cervix:	n/a
38	chr8:125463066-125463116	HIPEpiC	eye:	n/a
39	chr8:125463057-125463107	BE2_C	brain:	n/a
40	chr8:125463057-125463107	HNPCEpiC	eye:	n/a
41	chr8:125463066-125463116	AG09319	gingival:	n/a
42	chr8:125463057-125463107	Jurkat	blood:	n/a
43	chr8:125463057-125463107	SKMC	muscle:	n/a
44	chr8:125463057-125463107	AG04449	skin:	fetal
45	chr8:125463057-125463107	ovcar-3	ovarian:	n/a
46	chr8:125463066-125463116	ovcar-3	ovarian:	n/a
47	chr8:125463057-125463107	HRCEpiC	kidney:	n/a
48	chr8:125463057-125463107	AG09309	skin:	n/a
49	chr8:125463066-125463116	GM19239	blood:	n/a
50	chr8:125463066-125463116	HEK293	kidney:	embryo

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125460680..125466261-chr8:125549985..125555147,10	K562	blood:
2	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
3	chr8:125459763..125466594-chr8:125480347..125488760,16	K562	blood:
4	chr8:125051633..125053177-chr8:125461476..125463177,2	MCF-7	breast:
5	chr2:231280254..231281169-chr8:125462695..125463364,2	NB4	blood:
6	chr7:150781876..150784323-chr8:125460204..125463130,2	MCF-7	breast:
7	chr14:24609134..24611550-chr8:125461758..125464369,2	MCF-7	breast:
8	chr12:7072260..7073970-chr8:125462442..125465411,2	MCF-7	breast:
9	chr8:125461877..125466400-chr8:125548792..125551961,4	MCF-7	breast:
10	chr8:125461480..125466921-chr8:125547850..125552862,10	MCF-7	breast:
11	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:
12	chr8:125459427..125466261-chr8:125549985..125555147,10	K562	blood:

No data

Variant related genes	Relation type
TRMT12	TF binding region
TRMT12	CpG island
ENSG00000257084	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000181171	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000133612	Chromatin interaction
ENSG00000207708	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000067066	Chromatin interaction
ENSG00000254249	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000207713	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10091243	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10092569	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10106292	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11987932	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11991829	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12542293	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12548235	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28725399	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812471	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812472	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886003	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4128468	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132855	0.80[AMR][1000 genomes]
rs4269525	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4269526	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4871498	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6470243	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6470245	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6982197	0.89[EUR][1000 genomes]
rs6984985	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6987343	0.84[EUR][1000 genomes]
rs6993926	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7001480	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7005393	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7007115	0.87[EUR][1000 genomes]
rs7009290	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7013683	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7812331	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7812363	0.80[AMR][1000 genomes]
rs7812911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7825599	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7827791	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7830506	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1034768	chr8:125323011-125481733	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	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
4	nsv891430	chr8:125431030-125485027	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv891431	chr8:125437811-125485027	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv891432	chr8:125438093-125485027	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3812474	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs3812474	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	chr8:125462000-125463200	Active TSS	Adipose Nuclei	Adipose
2	chr8:125462000-125463200	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr8:125462000-125463400	Active TSS	Rectal Smooth Muscle	rectum
4	chr8:125462000-125463400	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr8:125462000-125463600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr8:125462000-125463600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:125462000-125463600	Active TSS	Brain Anterior Caudate	brain
8	chr8:125462000-125463600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:125462000-125463600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr8:125462000-125463600	Active TSS	Fetal Lung	lung
11	chr8:125462000-125463600	Active TSS	Ovary	ovary
12	chr8:125462000-125463600	Active TSS	Right Atrium	heart
13	chr8:125462000-125463800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:125462000-125463800	Active TSS	Aorta	Aorta
15	chr8:125462000-125463800	Active TSS	Colon Smooth Muscle	Colon
16	chr8:125462000-125464000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr8:125462000-125464200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr8:125462000-125464200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr8:125462000-125464600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:125462200-125463200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr8:125462200-125463200	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr8:125462200-125463400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:125462200-125463400	Active TSS	Brain Angular Gyrus	brain
24	chr8:125462200-125463400	Active TSS	Duodenum Mucosa	Duodenum
25	chr8:125462200-125463400	Active TSS	Fetal Muscle Trunk	muscle
26	chr8:125462200-125463400	Active TSS	Pancreas	Pancrea
27	chr8:125462200-125463600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:125462200-125463600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr8:125462200-125463600	Active TSS	Brain Cingulate Gyrus	brain
30	chr8:125462200-125463600	Active TSS	Brain Substantia Nigra	brain
31	chr8:125462200-125463600	Active TSS	Esophagus	oesophagus
32	chr8:125462200-125463600	Active TSS	Fetal Intestine Small	intestine
33	chr8:125462200-125463600	Active TSS	Fetal Stomach	stomach
34	chr8:125462200-125463600	Active TSS	Left Ventricle	heart
35	chr8:125462200-125463600	Active TSS	Stomach Smooth Muscle	stomach
36	chr8:125462200-125463600	Active TSS	NH-A	brain
37	chr8:125462200-125463800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr8:125462200-125463800	Active TSS	Fetal Intestine Large	intestine
39	chr8:125462200-125463800	Active TSS	Fetal Kidney	kidney
40	chr8:125462200-125463800	Active TSS	Psoas Muscle	Psoas
41	chr8:125462200-125463800	Active TSS	Right Ventricle	heart
42	chr8:125462200-125463800	Active TSS	A549	lung
43	chr8:125462200-125463800	Active TSS	GM12878-XiMat	blood
44	chr8:125462200-125463800	Active TSS	HSMMtube	muscle
45	chr8:125462200-125463800	Active TSS	NHLF	lung
46	chr8:125462200-125464000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr8:125462200-125464200	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr8:125462200-125464200	Flanking Active TSS	Liver	Liver
49	chr8:125462200-125464200	Active TSS	Colonic Mucosa	Colon
50	chr8:125462400-125463200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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