Variant report

Variant	rs56000812
Chromosome Location	chr1:151899104-151899105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151897183..151899597-chr1:151964154..151966740,2	MCF-7	breast:
2	chr1:151898614..151900829-chr1:151904276..151907229,3	K562	blood:
3	chr1:151882722..151885720-chr1:151898176..151900104,2	MCF-7	breast:
4	chr1:151896761..151899276-chr1:152001474..152003211,2	MCF-7	breast:
5	chr1:151879281..151886788-chr1:151893548..151899266,9	MCF-7	breast:
6	chr1:151896603..151899369-chr1:152019666..152021971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10494270	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204906	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204919	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11204920	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11582739	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12083193	0.85[AMR][1000 genomes]
rs12095483	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566232	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16833668	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16833669	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16833670	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16833728	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16833743	0.85[AMR][1000 genomes]
rs1844543	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2337685	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2337686	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2338206	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415528	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932580	0.85[ASN][1000 genomes]
rs3791153	0.85[AMR][1000 genomes]
rs4845719	0.84[AMR][1000 genomes]
rs56028913	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56078223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170235	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56313205	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57674198	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57785325	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58087484	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61814883	0.83[AMR][1000 genomes]
rs61817695	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817697	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61817719	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61817720	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61817722	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61817723	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817724	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61817725	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6587632	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587633	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587634	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587635	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6587636	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6587637	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6587638	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6657658	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6659662	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662602	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662611	0.84[AMR][1000 genomes]
rs6662728	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6663064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6672064	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675930	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6678672	0.87[AMR][1000 genomes]
rs6682605	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6684114	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6684312	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6686874	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690449	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6693388	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6693396	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6693901	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6695324	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6701374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703448	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703465	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72694840	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535002	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7538652	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7541099	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7554832	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7554859	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs902313	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs971887	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9943221	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9943251	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56000812	THEM4	cis	multi-tissue	Pritchard
rs56000812	THEM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151897800-151899400	Enhancers	Fetal Intestine Small	intestine
2	chr1:151898200-151899200	Enhancers	Fetal Intestine Large	intestine
3	chr1:151898200-151900600	Enhancers	GM12878-XiMat	blood
4	chr1:151898200-151902600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:151898400-151899200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:151898400-151899600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:151899000-151899200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:151899000-151899400	Enhancers	K562	blood

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