Variant report

Variant	rs6987343
Chromosome Location	chr8:125559807-125559808
allele	A/C
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	POLR2A	chr8:125559464-125559923	HepG2	liver:	n/a	n/a
2	POLR2A	chr8:125559742-125559926	K562	blood:	n/a	n/a
3	STAT3	chr8:125559729-125559813	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125485694..125488622-chr8:125558773..125560275,2	MCF-7	breast:
2	chr8:125557600..125560665-chr8:125561474..125566163,6	MCF-7	breast:

Variant related genes	Relation type
NDUFB9	TF binding region
ENSG00000245149	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000170881	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10091243	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10092569	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10106292	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11991829	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12542293	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12548235	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28725399	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3812471	0.92[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3812472	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs3812474	0.84[EUR][1000 genomes]
rs3812475	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs3886003	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4128468	0.93[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4269525	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4269526	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4870901	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4871498	0.92[CEU][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4871499	0.81[EUR][1000 genomes]
rs6470245	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6982197	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]
rs6984985	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6993926	0.89[EUR][1000 genomes]
rs7001480	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7005393	0.82[EUR][1000 genomes]
rs7007115	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7009290	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7013683	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7812331	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7812911	0.90[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs7825599	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7827791	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7830506	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6987343	ZHX2	cis	parietal	SCAN
rs6987343	TRMT12	cis	lymphoblastoid	seeQTL
rs6987343	TRMT12	Cis_1M	lymphoblastoid	RTeQTL
rs6987343	TRMT12	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125552200-125565200	Weak transcription	Small Intestine	intestine
2	chr8:125552200-125565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:125552200-125568600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:125553400-125568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:125553400-125568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
8	chr8:125553600-125566400	Strong transcription	A549	lung
9	chr8:125553600-125566800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
12	chr8:125554000-125572400	Strong transcription	Thymus	Thymus
13	chr8:125554000-125574000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:125554200-125566800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:125554200-125568600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:125554200-125570000	Strong transcription	Fetal Thymus	thymus
17	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr8:125554400-125560200	Strong transcription	Osteobl	bone
19	chr8:125554400-125560600	Strong transcription	Fetal Lung	lung
20	chr8:125554400-125561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:125554400-125567400	Strong transcription	Colon Smooth Muscle	Colon
22	chr8:125554400-125568200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr8:125554400-125568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:125554400-125569000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:125554400-125574200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr8:125554400-125575400	Strong transcription	Primary B cells from cord blood	blood
27	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
28	chr8:125554600-125560000	Strong transcription	Adipose Nuclei	Adipose
29	chr8:125554600-125560000	Weak transcription	Right Atrium	heart
30	chr8:125554600-125560200	Strong transcription	HepG2	liver
31	chr8:125554600-125560600	Strong transcription	Liver	Liver
32	chr8:125554600-125562200	Strong transcription	Brain Germinal Matrix	brain
33	chr8:125554600-125562400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr8:125554600-125562600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr8:125554600-125565400	Strong transcription	NH-A	brain
36	chr8:125554600-125566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr8:125554600-125566400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr8:125554600-125566600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr8:125554600-125566600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr8:125554600-125568000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr8:125554600-125574000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:125554600-125575000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr8:125554600-125575800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr8:125554800-125560000	Strong transcription	Brain Anterior Caudate	brain
45	chr8:125554800-125562400	Strong transcription	Brain Hippocampus Middle	brain
46	chr8:125554800-125562600	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr8:125554800-125564400	Strong transcription	HSMMtube	muscle
48	chr8:125554800-125564800	Strong transcription	Hela-S3	cervix
49	chr8:125554800-125566800	Strong transcription	HSMM	muscle
50	chr8:125554800-125569200	Strong transcription	Rectal Mucosa Donor 31	rectum

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