Variant report

Variant	rs4301437
Chromosome Location	chr8:125460073-125460074
allele	A/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	ESR1	chr8:125460010-125460414	T-47D	breast:	n/a	n/a
2	MYC	chr8:125459437-125460282	K562	blood:	n/a	chr8:125459622-125459632
3	GATA3	chr8:125460006-125460520	T-47D	breast:	n/a	n/a
4	GATA3	chr8:125460005-125460541	T-47D	breast:	n/a	n/a
5	NR2F2	chr8:125459909-125460486	MCF-7	breast:	n/a	n/a
6	JUN	chr8:125459121-125460178	K562	blood:	n/a	n/a
7	EP300	chr8:125459951-125460555	T-47D	breast:	n/a	chr8:125460279-125460293 chr8:125460265-125460275
8	FOXA1	chr8:125459936-125460506	T-47D	breast:	n/a	chr8:125460264-125460279 chr8:125460186-125460198
9	EP300	chr8:125460004-125460515	T-47D	breast:	n/a	chr8:125460279-125460293 chr8:125460265-125460275
10	FOXA1	chr8:125459996-125460498	T-47D	breast:	n/a	chr8:125460264-125460279 chr8:125460186-125460198

No.	Distal block	Cell Line	Cell type
1	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
2	chr8:125459763..125466594-chr8:125480347..125488760,16	K562	blood:
3	chr8:124792624..124795520-chr8:125459150..125461003,2	K562	blood:
4	chr8:125448058..125451036-chr8:125458911..125461802,2	MCF-7	breast:
5	chr8:125458816..125460797-chr8:125549847..125552574,2	MCF-7	breast:
6	chr8:125458853..125460594-chr8:125466039..125468256,2	K562	blood:
7	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:
8	chr8:125459427..125466261-chr8:125549985..125555147,10	K562	blood:

Variant related genes	Relation type
TRMT12	TF binding region
ENSG00000245149	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000176853	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11542673	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11986208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899649	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16899653	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3829038	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4128469	0.88[JPT][hapmap]
rs4132855	0.88[JPT][hapmap]
rs4870899	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4870902	0.92[EUR][1000 genomes]
rs4871493	0.87[ASN][1000 genomes]
rs4871496	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4871497	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55759812	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55872747	0.87[ASN][1000 genomes]
rs55946925	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56158167	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56291877	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67764028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7005580	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72713064	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72713066	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72713068	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713072	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713074	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713078	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72713081	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713082	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713088	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72713090	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72713094	0.88[EUR][1000 genomes]
rs72713101	0.92[EUR][1000 genomes]
rs72714703	0.92[EUR][1000 genomes]
rs72714704	0.92[EUR][1000 genomes]
rs72714706	0.92[EUR][1000 genomes]
rs72714707	0.92[EUR][1000 genomes]
rs72714712	0.92[EUR][1000 genomes]
rs7812363	0.88[JPT][hapmap]

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
rs4301437	TRMT12	cis	multi-tissue	Pritchard
rs4301437	TRMT12	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125450800-125462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:125453200-125461800	Weak transcription	HMEC	breast
3	chr8:125456200-125462200	Weak transcription	Psoas Muscle	Psoas
4	chr8:125459000-125460200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:125459200-125460400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:125459200-125460400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:125459200-125460400	Enhancers	NHDF-Ad	bronchial
8	chr8:125459200-125460600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr8:125459200-125461000	Enhancers	K562	blood
10	chr8:125459400-125460200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:125459400-125460400	Enhancers	HSMMtube	muscle
12	chr8:125459400-125460600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr8:125459400-125462000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr8:125459600-125460200	Enhancers	HSMM	muscle
15	chr8:125459600-125460400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr8:125459800-125460200	Enhancers	HepG2	liver
17	chr8:125459800-125461400	Enhancers	Colonic Mucosa	Colon
18	chr8:125459800-125462000	Weak transcription	Adipose Nuclei	Adipose
19	chr8:125459800-125462200	Weak transcription	NHLF	lung
20	chr8:125460000-125460600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:125460000-125460600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr8:125460000-125460800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr8:125460000-125462000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr8:125460000-125462000	Weak transcription	Hela-S3	cervix
25	chr8:125460000-125462000	Weak transcription	Osteobl	bone
26	chr8:125460000-125462200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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