Variant report

Variant	rs4257989
Chromosome Location	chr8:125388560-125388561
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125383110..125385797-chr8:125388504..125391185,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164983	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10091430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096657	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10105192	0.94[ASN][1000 genomes]
rs10111787	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956175	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11997689	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12680422	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12680423	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16899562	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16899577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17297352	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17369737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17369758	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28456315	0.97[ASN][1000 genomes]
rs28460280	0.97[ASN][1000 genomes]
rs28536158	0.97[ASN][1000 genomes]
rs28538795	0.97[ASN][1000 genomes]
rs28562339	0.97[ASN][1000 genomes]
rs28594441	0.97[ASN][1000 genomes]
rs28694575	0.97[ASN][1000 genomes]
rs28716042	0.91[ASN][1000 genomes]
rs28721926	0.97[ASN][1000 genomes]
rs28827823	0.97[ASN][1000 genomes]
rs4128778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355753	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4364615	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4366066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368958	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376483	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394374	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4406374	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4503079	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527851	0.81[CEU][hapmap]
rs4601290	0.80[EUR][1000 genomes]
rs4617135	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55679493	1.00[ASN][1000 genomes]
rs55931807	0.94[ASN][1000 genomes]
rs56036293	0.94[ASN][1000 genomes]
rs56142132	0.94[ASN][1000 genomes]
rs56166945	1.00[ASN][1000 genomes]
rs56202566	0.94[ASN][1000 genomes]
rs56225520	0.97[ASN][1000 genomes]
rs56893629	1.00[ASN][1000 genomes]
rs58908685	1.00[ASN][1000 genomes]
rs6984676	0.83[ASN][1000 genomes]
rs6984691	0.83[ASN][1000 genomes]
rs7005950	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7015493	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs73332159	0.94[ASN][1000 genomes]
rs73332190	0.97[ASN][1000 genomes]
rs73332191	0.89[ASN][1000 genomes]
rs73333910	0.97[ASN][1000 genomes]
rs73333911	0.97[ASN][1000 genomes]
rs73333937	1.00[ASN][1000 genomes]
rs73333948	1.00[ASN][1000 genomes]
rs73333990	0.94[ASN][1000 genomes]
rs73333993	0.94[ASN][1000 genomes]
rs73333994	0.94[ASN][1000 genomes]
rs73336155	0.94[ASN][1000 genomes]
rs73336165	0.94[ASN][1000 genomes]
rs73336173	0.94[ASN][1000 genomes]
rs73336179	0.94[ASN][1000 genomes]
rs73336181	0.94[ASN][1000 genomes]
rs73336185	0.94[ASN][1000 genomes]
rs73336195	0.94[ASN][1000 genomes]
rs73336202	0.94[ASN][1000 genomes]
rs73337903	0.94[ASN][1000 genomes]
rs73337904	0.94[ASN][1000 genomes]
rs7386980	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7387197	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7388185	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462023	0.82[ASN][1000 genomes]
rs7819589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7835963	0.94[ASN][1000 genomes]
rs7836478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv521356	chr8:125309055-125404763	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	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
4	nsv527751	chr8:125338216-125431030	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4257989	TRMT12	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125386000-125389200	Enhancers	Fetal Heart	heart
2	chr8:125387000-125389200	Enhancers	Pancreas	Pancrea
3	chr8:125387400-125390000	Enhancers	HSMM	muscle
4	chr8:125387600-125389600	Enhancers	HSMMtube	muscle
5	chr8:125388000-125388800	Enhancers	Fetal Muscle Leg	muscle
6	chr8:125388000-125389200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr8:125388000-125389400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:125388000-125389600	Enhancers	Primary hematopoietic stem cells	blood
9	chr8:125388200-125389600	Enhancers	HUVEC	blood vessel
10	chr8:125388400-125388600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr8:125388400-125388800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:125388400-125388800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr8:125388400-125388800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr8:125388400-125389200	Enhancers	Pancreatic Islets	Pancreatic Islet

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