Variant report

Variant	rs12542260
Chromosome Location	chr8:125502440-125502441
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125501973..125504585-chr8:125508196..125511474,3	MCF-7	breast:
2	chr8:125501162..125503878-chr8:125549908..125551585,2	K562	blood:
3	chr4:80053807..80054491-chr8:125501594..125502544,2	MCF-7	breast:
4	chr8:125501995..125503698-chr8:125571689..125573791,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF139-1	chr8:125500751-125502523	ENSG00000253106.1

Variant related genes	Relation type
ENSG00000147684	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10956184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10956185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10956189	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11556913	0.81[ASN][1000 genomes]
rs12544211	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12544621	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12545267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12546906	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12548836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12550707	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12550827	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28576577	1.00[LWK][hapmap]
rs4128469	0.88[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4512366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4551335	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4602869	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4870898	0.80[EUR][1000 genomes]
rs5004281	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56942034	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57941917	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62527880	0.81[EUR][1000 genomes]
rs62527883	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62527884	0.81[EUR][1000 genomes]
rs62527886	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62527901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62527908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62527910	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6987213	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6987358	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7009847	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72713049	0.81[EUR][1000 genomes]
rs7830325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7834203	0.81[EUR][1000 genomes]
rs7836802	0.82[EUR][1000 genomes]
rs7845008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12542260	TRMT12	cis	Whole Blood	GTEx
rs12542260	TRIB1	cis	parietal	SCAN
rs12542260	ZHX2	cis	cerebellum	SCAN
rs12542260	ZHX2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488000-125503400	Weak transcription	Spleen	Spleen
2	chr8:125488200-125515800	Weak transcription	Lung	lung
3	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:125489000-125503400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:125489000-125505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:125489000-125519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:125489000-125531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:125489000-125541200	Weak transcription	Gastric	stomach
9	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
10	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr8:125496000-125512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:125496800-125503400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:125496800-125503400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr8:125496800-125513200	Weak transcription	Brain Angular Gyrus	brain
16	chr8:125496800-125521200	Weak transcription	Fetal Heart	heart
17	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr8:125497600-125505200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr8:125497800-125504000	Strong transcription	Primary B cells from cord blood	blood
20	chr8:125497800-125506200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:125498000-125502600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:125498000-125502600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr8:125498000-125503600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr8:125498000-125503800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr8:125498000-125503800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr8:125498000-125504000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr8:125498000-125504000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr8:125498000-125504000	Strong transcription	Fetal Thymus	thymus
29	chr8:125498000-125504200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr8:125498000-125504400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr8:125498000-125504600	Strong transcription	Primary T cells from cord blood	blood
32	chr8:125498000-125504600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr8:125498000-125505000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr8:125498000-125505800	Strong transcription	Dnd41	blood
35	chr8:125498000-125506200	Strong transcription	Fetal Intestine Large	intestine
36	chr8:125498000-125506600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr8:125498000-125506800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:125498200-125502600	Strong transcription	HMEC	breast
39	chr8:125498200-125502800	Strong transcription	Liver	Liver
40	chr8:125498200-125503400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:125498200-125503800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr8:125498200-125503800	Strong transcription	Placenta	Placenta
43	chr8:125498200-125504000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr8:125498200-125504200	Strong transcription	Osteobl	bone
45	chr8:125498200-125504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr8:125498200-125504800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr8:125498200-125506000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr8:125498200-125506000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr8:125498200-125507600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr8:125498200-125508000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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