Variant report

Variant	rs12091720
Chromosome Location	chr1:76186949-76186950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:76186784-76187082	GM12878	blood:	n/a	n/a
2	BHLHE40	chr1:76186904-76187053	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:76186738-76187119	GM12878	blood:	n/a	n/a
4	MAX	chr1:76186831-76187101	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76171538..76176296-chr1:76182594..76187669,7	K562	blood:
2	chr1:76183392..76187625-chr1:76187644..76191545,4	MCF-7	breast:
3	chr1:76186929..76188557-chr16:30758246..30760309,2	K562	blood:
4	chr1:76184568..76187287-chr1:76187578..76190885,3	MCF-7	breast:
5	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:

No data

Variant related genes	Relation type
ACADM	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000156873	Chromatin interaction
ENSG00000201487	Chromatin interaction
ENSG00000117054	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000057468	Chromatin interaction
ENSG00000207241	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1061337	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10873685	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11161437	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161468	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11161493	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11161510	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11161511	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11161515	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11161521	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11163924	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146574	0.92[EUR][1000 genomes]
rs1146579	0.92[EUR][1000 genomes]
rs1146580	0.92[EUR][1000 genomes]
rs1146581	0.92[EUR][1000 genomes]
rs1146588	0.91[EUR][1000 genomes]
rs12094842	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12123977	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12126481	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12126607	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12127402	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12134854	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12136754	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1250874	0.92[EUR][1000 genomes]
rs1251075	0.91[EUR][1000 genomes]
rs1303169	0.90[EUR][1000 genomes]
rs1313071	0.91[EUR][1000 genomes]
rs1498312	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498315	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498316	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498317	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611823	0.91[EUR][1000 genomes]
rs1612097	0.92[EUR][1000 genomes]
rs1694419	0.92[EUR][1000 genomes]
rs1694424	0.87[EUR][1000 genomes]
rs17587071	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1767455	0.87[EUR][1000 genomes]
rs1767456	0.92[EUR][1000 genomes]
rs1767458	0.92[EUR][1000 genomes]
rs1770511	0.91[EUR][1000 genomes]
rs1855136	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1858536	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1890451	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1890452	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2066183	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211717	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211718	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211737	0.89[ASN][1000 genomes]
rs2153126	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2173378	0.92[EUR][1000 genomes]
rs2185152	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2185435	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2185436	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2211080	0.87[EUR][1000 genomes]
rs2275378	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2788654	0.92[EUR][1000 genomes]
rs28602663	0.92[EUR][1000 genomes]
rs380075	0.84[ASN][1000 genomes]
rs3818855	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs392691	0.89[ASN][1000 genomes]
rs4559448	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4646961	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4949674	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4949872	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949874	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949875	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949876	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949877	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4949879	0.92[EUR][1000 genomes]
rs56267813	0.83[EUR][1000 genomes]
rs56352044	0.84[EUR][1000 genomes]
rs57186386	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60378926	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61289992	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61622554	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61797339	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61797340	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61799967	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61799988	0.87[EUR][1000 genomes]
rs61799990	0.88[EUR][1000 genomes]
rs6593514	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6593515	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6593585	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6688749	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72686191	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7513363	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7513559	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516122	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7516226	0.92[EUR][1000 genomes]
rs7518038	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7524467	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7533888	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7534754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535991	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539246	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7541058	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7544117	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546641	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7548962	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549167	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7550974	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7552404	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7554984	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs942270	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662166	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv871572	chr1:76161889-76208488	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12091720	MSH4	cis	Artery Tibial	GTEx
rs12091720	ACADM	cis	Whole Blood	GTEx
rs12091720	ACADM	cis	Muscle Skeletal	GTEx
rs12091720	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76184200-76189000	Weak transcription	Esophagus	oesophagus
2	chr1:76184600-76187200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:76185600-76187200	Enhancers	K562	blood
4	chr1:76185600-76187600	Enhancers	Fetal Intestine Large	intestine
5	chr1:76185800-76187200	Enhancers	Fetal Thymus	thymus
6	chr1:76186000-76187400	Enhancers	HepG2	liver
7	chr1:76186000-76188600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:76186000-76189600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:76186200-76187400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:76186200-76188600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:76186200-76189200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:76186200-76189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:76186400-76187200	Enhancers	Thymus	Thymus
14	chr1:76186600-76187000	Weak transcription	Fetal Intestine Small	intestine
15	chr1:76186600-76187200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:76186600-76187400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:76186600-76187600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:76186800-76187000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:76186800-76187200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr1:76186800-76187400	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:76186800-76189400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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