Variant report

Variant	rs7013683
Chromosome Location	chr8:125517960-125517961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125485559..125487740-chr8:125517609..125520546,3	MCF-7	breast:
2	chr8:125484977..125488762-chr8:125516872..125524765,8	MCF-7	breast:
3	chr8:125500685..125503615-chr8:125517583..125520355,2	K562	blood:
4	chr8:125515035..125519543-chr8:125547357..125551225,5	MCF-7	breast:
5	chr8:125499578..125501276-chr8:125515808..125518210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147687	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000253106	Chromatin interaction
ENSG00000170881	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10091243	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10092569	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10106292	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11987932	0.83[EUR][1000 genomes]
rs11991829	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12542293	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12548235	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28725399	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812471	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812472	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812474	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812475	0.80[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3886003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4128468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132855	0.92[MEX][hapmap]
rs4269525	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4269526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4870901	0.83[AMR][1000 genomes]
rs4871498	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]
rs6470243	0.80[EUR][1000 genomes]
rs6470245	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6982197	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]
rs6984985	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6987343	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs6993926	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7001480	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7005393	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7007115	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7009290	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7010411	0.90[JPT][hapmap]
rs7812331	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7812911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7825599	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827791	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7830506	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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
rs7013683	TRMT12	cis	uninvolved skin	skin_eQTL
rs7013683	ZHX2	cis	parietal	SCAN
rs7013683	TRMT12	cis	lymphoblastoid	seeQTL
rs7013683	TRMT12	cis	Whole Blood	GTEx
rs7013683	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr8:125489000-125519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:125489000-125531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:125489000-125541200	Weak transcription	Gastric	stomach
5	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
6	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr8:125496800-125521200	Weak transcription	Fetal Heart	heart
9	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:125499000-125537200	Weak transcription	Esophagus	oesophagus
11	chr8:125500000-125526200	Weak transcription	Colonic Mucosa	Colon
12	chr8:125500000-125538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr8:125500000-125538400	Weak transcription	Psoas Muscle	Psoas
14	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
15	chr8:125500200-125530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr8:125500400-125526400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr8:125501600-125524600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:125501600-125535000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr8:125503800-125518800	Weak transcription	Brain Hippocampus Middle	brain
21	chr8:125504000-125518800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr8:125504000-125518800	Weak transcription	Brain Substantia Nigra	brain
23	chr8:125504000-125521200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr8:125504000-125524800	Weak transcription	Pancreas	Pancrea
25	chr8:125504000-125525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:125504000-125525800	Weak transcription	NHLF	lung
27	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
28	chr8:125504400-125518800	Weak transcription	Ovary	ovary
29	chr8:125505800-125538600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr8:125506000-125538600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr8:125507600-125522000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr8:125508400-125532200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr8:125510200-125536800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:125510400-125536200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr8:125510800-125532200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr8:125511600-125536400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr8:125512000-125536000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:125512200-125528000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:125512200-125530400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr8:125512200-125531600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr8:125512400-125519800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr8:125512400-125521800	Strong transcription	Fetal Thymus	thymus
43	chr8:125512400-125522000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:125512400-125522600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr8:125512400-125528200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr8:125512400-125535800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr8:125512400-125536400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr8:125512600-125520000	Strong transcription	Fetal Muscle Leg	muscle
49	chr8:125512600-125522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:125512600-125522600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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