Variant report

Variant	rs4132855
Chromosome Location	chr8:125462121-125462122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr8:125461952-125464799	SK-N-SH	brain:	n/a	chr8:125462986-125463001
2	CTCF	chr8:125462080-125462230	NHLF	lung:	n/a	n/a
3	HCFC1	chr8:125461831-125464659	Hela-S3	cervix:	n/a	n/a
4	SRF	chr8:125461928-125463490	HCT-116	colon:	n/a	chr8:125462500-125462518
5	SRF	chr8:125461938-125463763	MCF-7	breast:	n/a	chr8:125462500-125462518
6	ZMIZ1	chr8:125462095-125462220	K562	blood:	n/a	n/a
7	SRF	chr8:125461936-125463497	HCT-116	colon:	n/a	chr8:125462500-125462518
8	SRF	chr8:125461983-125463783	MCF-7	breast:	n/a	chr8:125462500-125462518

No data

(count:11 , 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	chr8:125209307..125211794-chr8:125460227..125463007,2	K562	blood:
6	chr7:150781876..150784323-chr8:125460204..125463130,2	MCF-7	breast:
7	chr14:24609134..24611550-chr8:125461758..125464369,2	MCF-7	breast:
8	chr8:125461877..125466400-chr8:125548792..125551961,4	MCF-7	breast:
9	chr8:125461480..125466921-chr8:125547850..125552862,10	MCF-7	breast:
10	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:
11	chr8:125459427..125466261-chr8:125549985..125555147,10	K562	blood:

No data

Variant related genes	Relation type
TRMT12	TF binding region
ENSG00000133612	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000181171	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000254249	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000245149	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11556913	0.87[EUR][1000 genomes]
rs11986208	0.88[JPT][hapmap]
rs16899649	0.82[JPT][hapmap]
rs16899653	0.82[JPT][hapmap]
rs3812471	0.92[MEX][hapmap]
rs3812472	0.92[MEX][hapmap]
rs3812474	0.80[AMR][1000 genomes]
rs3812475	0.92[MEX][hapmap];0.80[AMR][1000 genomes]
rs3829038	0.82[JPT][hapmap]
rs4128468	0.83[MEX][hapmap]
rs4128469	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4301437	0.88[JPT][hapmap]
rs4870898	0.92[ASN][1000 genomes]
rs62527880	0.93[ASN][1000 genomes]
rs62527881	0.85[ASN][1000 genomes]
rs62527882	0.89[ASN][1000 genomes]
rs62527884	0.92[ASN][1000 genomes]
rs7013683	0.92[MEX][hapmap]
rs72713049	0.92[ASN][1000 genomes]
rs7812363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7812911	0.80[AMR][1000 genomes]
rs7826104	0.92[ASN][1000 genomes]
rs7830506	0.91[MEX][hapmap]
rs7834203	0.90[ASN][1000 genomes]
rs7836802	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4132855	KIAA0196	cis	parietal	SCAN
rs4132855	TRMT12	cis	multi-tissue	Pritchard
rs4132855	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs4132855	TRMT12	cis	cerebellum	SCAN
rs4132855	TRIB1	cis	parietal	SCAN
rs4132855	TRMT12	cis	Whole Blood	GTEx
rs4132855	TRMT12	cis	Skin Sun Exposed Lower leg	GTEx
rs4132855	TRMT12	cis	uninvolved skin	skin_eQTL
rs4132855	ZNF572	cis	cerebellum	SCAN
rs4132855	TRMT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125450800-125462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:125456200-125462200	Weak transcription	Psoas Muscle	Psoas
3	chr8:125459800-125462200	Weak transcription	NHLF	lung
4	chr8:125460000-125462200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:125460200-125462200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:125460200-125462400	Weak transcription	HSMM	muscle
7	chr8:125460400-125462200	Weak transcription	HSMMtube	muscle
8	chr8:125460400-125462400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:125460600-125462200	Weak transcription	Placenta	Placenta
10	chr8:125460600-125462400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:125460600-125462600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:125460600-125462600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr8:125460800-125462600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:125461200-125462200	Enhancers	HepG2	liver
15	chr8:125461400-125462200	Weak transcription	Colonic Mucosa	Colon
16	chr8:125461600-125462600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr8:125461600-125463000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr8:125461800-125462200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr8:125462000-125462200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr8:125462000-125462200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr8:125462000-125462200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr8:125462000-125462200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr8:125462000-125462200	Enhancers	Primary B cells from cord blood	blood
24	chr8:125462000-125462200	Enhancers	Primary B cells from peripheral blood	blood
25	chr8:125462000-125462200	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr8:125462000-125462200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr8:125462000-125462200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr8:125462000-125462200	Enhancers	Liver	Liver
29	chr8:125462000-125462200	Enhancers	Brain Cingulate Gyrus	brain
30	chr8:125462000-125462200	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr8:125462000-125462200	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr8:125462000-125462200	Enhancers	Fetal Heart	heart
33	chr8:125462000-125462200	Enhancers	Fetal Kidney	kidney
34	chr8:125462000-125462200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr8:125462000-125462200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr8:125462000-125462200	Enhancers	Right Ventricle	heart
37	chr8:125462000-125462200	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr8:125462000-125462200	Flanking Active TSS	A549	lung
39	chr8:125462000-125462200	Enhancers	GM12878-XiMat	blood
40	chr8:125462000-125462200	Enhancers	Osteobl	bone
41	chr8:125462000-125462400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr8:125462000-125462400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr8:125462000-125462400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr8:125462000-125462400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr8:125462000-125462400	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr8:125462000-125462400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr8:125462000-125462400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr8:125462000-125462400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr8:125462000-125462400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr8:125462000-125462400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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