Variant report

Variant	rs28602663
Chromosome Location	chr1:76235355-76235356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76234782..76236284-chr1:76243274..76245425,2	K562	blood:
2	chr1:76216562..76219255-chr1:76235194..76236750,2	K562	blood:
3	chr1:76235199..76237573-chr1:76250494..76252848,2	K562	blood:
4	chr1:76230100..76233038-chr1:76235257..76238207,3	K562	blood:
5	chr1:76230023..76233011-chr1:76235018..76236757,2	K562	blood:

Variant related genes	Relation type
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1061337	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10873685	0.93[EUR][1000 genomes]
rs11161437	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11161468	0.91[EUR][1000 genomes]
rs11161493	0.87[EUR][1000 genomes]
rs11161510	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161511	0.93[EUR][1000 genomes]
rs11161515	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161521	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11161620	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11161626	0.81[EUR][1000 genomes]
rs11163924	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1146574	0.86[EUR][1000 genomes]
rs1146579	0.86[EUR][1000 genomes]
rs1146580	0.86[EUR][1000 genomes]
rs1146581	0.86[EUR][1000 genomes]
rs1146588	0.87[EUR][1000 genomes]
rs12091720	0.92[EUR][1000 genomes]
rs12093623	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12094842	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12122939	0.80[AMR][1000 genomes]
rs12123977	0.93[EUR][1000 genomes]
rs12126481	0.89[EUR][1000 genomes]
rs12126607	0.93[EUR][1000 genomes]
rs12127078	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12127402	0.93[EUR][1000 genomes]
rs12134854	0.80[EUR][1000 genomes]
rs12136754	0.88[EUR][1000 genomes]
rs1250874	0.86[EUR][1000 genomes]
rs1251075	0.85[EUR][1000 genomes]
rs1303169	0.84[EUR][1000 genomes]
rs1313071	0.85[EUR][1000 genomes]
rs1498312	0.90[EUR][1000 genomes]
rs1498315	0.87[EUR][1000 genomes]
rs1498316	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1498317	0.80[EUR][1000 genomes]
rs1611823	0.85[EUR][1000 genomes]
rs1612097	0.86[EUR][1000 genomes]
rs1694419	0.86[EUR][1000 genomes]
rs1694424	0.83[EUR][1000 genomes]
rs17587071	0.94[EUR][1000 genomes]
rs1767455	0.83[EUR][1000 genomes]
rs1767456	0.86[EUR][1000 genomes]
rs1767458	0.86[EUR][1000 genomes]
rs1770511	0.87[EUR][1000 genomes]
rs1855136	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1858536	0.82[EUR][1000 genomes]
rs1890451	0.93[EUR][1000 genomes]
rs1890452	0.87[EUR][1000 genomes]
rs2066183	0.80[EUR][1000 genomes]
rs2153126	0.87[EUR][1000 genomes]
rs2173378	0.86[EUR][1000 genomes]
rs2185152	0.93[EUR][1000 genomes]
rs2185435	0.87[EUR][1000 genomes]
rs2185436	0.87[EUR][1000 genomes]
rs2211080	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275378	0.87[EUR][1000 genomes]
rs2788654	0.86[EUR][1000 genomes]
rs3818855	0.87[EUR][1000 genomes]
rs4559448	0.93[EUR][1000 genomes]
rs4646961	0.93[EUR][1000 genomes]
rs4949674	0.93[EUR][1000 genomes]
rs4949677	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4949872	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4949874	0.87[EUR][1000 genomes]
rs4949875	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4949876	0.89[EUR][1000 genomes]
rs4949877	0.93[EUR][1000 genomes]
rs4949879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267813	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56352044	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57186386	0.87[EUR][1000 genomes]
rs5745336	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5745363	0.82[AMR][1000 genomes]
rs60378926	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61289992	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61622554	0.94[EUR][1000 genomes]
rs61797339	0.92[EUR][1000 genomes]
rs61797340	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61799967	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61799988	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61799990	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593514	0.87[EUR][1000 genomes]
rs6593515	0.87[EUR][1000 genomes]
rs6593585	0.81[EUR][1000 genomes]
rs6688749	0.84[EUR][1000 genomes]
rs72686191	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7513559	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7516122	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7516226	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518038	0.86[EUR][1000 genomes]
rs7524467	0.93[EUR][1000 genomes]
rs7533888	0.87[EUR][1000 genomes]
rs7534754	0.92[EUR][1000 genomes]
rs7535991	0.82[EUR][1000 genomes]
rs7539246	0.93[EUR][1000 genomes]
rs7541058	0.84[EUR][1000 genomes]
rs7544117	0.82[EUR][1000 genomes]
rs7546641	0.81[EUR][1000 genomes]
rs7547056	0.80[AMR][1000 genomes]
rs7548962	0.81[EUR][1000 genomes]
rs7549167	0.81[EUR][1000 genomes]
rs7550974	0.87[EUR][1000 genomes]
rs7552404	0.81[EUR][1000 genomes]
rs7554984	0.84[EUR][1000 genomes]
rs942270	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9662166	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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	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
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv2763563	chr1:76229839-76245374	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28602663	ACADM	cis	Whole Blood	GTEx
rs28602663	ACADM	cis	Muscle Skeletal	GTEx
rs28602663	ACADM	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76221200-76238400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:76222000-76236600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:76222000-76237000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:76223800-76236600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:76227400-76249800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:76227800-76239600	Weak transcription	GM12878-XiMat	blood
7	chr1:76232800-76236600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:76232800-76243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:76234000-76236600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:76234000-76241000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:76234600-76237600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:76234600-76237600	Weak transcription	NHEK	skin
13	chr1:76234600-76237800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:76234600-76241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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