Variant report

Variant	rs28730907
Chromosome Location	chr3:160382972-160382973
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160281841..160283673-chr3:160382473..160384132,2	K562	blood:
2	chr3:160378138..160380305-chr3:160382789..160386961,3	K562	blood:
3	chr3:160377138..160379638-chr3:160382685..160384289,2	K562	blood:
4	chr3:160382522..160384796-chr3:160388142..160391052,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10936207	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936208	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10936209	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936210	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11709300	0.87[EUR][1000 genomes]
rs11714916	0.85[AMR][1000 genomes]
rs11927913	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12490985	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13065289	0.85[EUR][1000 genomes]
rs13095931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317085	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1403045	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1522285	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16831337	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17236586	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1879797	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1980277	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2178452	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28544045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34362576	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34949451	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35308461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35480231	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35664264	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35867836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36118017	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3946273	0.94[EUR][1000 genomes]
rs4133253	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4679659	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679660	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679909	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679910	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62272215	0.87[EUR][1000 genomes]
rs62272216	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272217	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272218	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272219	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272220	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773962	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6774379	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6774566	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6776873	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777739	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6779581	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779671	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787452	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797760	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798462	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6801373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803670	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6806755	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7610939	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7632884	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28730907	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160372600-160385200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:160379200-160383800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160379600-160383400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:160379800-160383000	Weak transcription	Dnd41	blood
5	chr3:160379800-160383600	Weak transcription	Thymus	Thymus
6	chr3:160381000-160383200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:160381000-160383600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:160382400-160383600	Enhancers	Hela-S3	cervix
9	chr3:160382400-160385400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:160382600-160383600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:160382600-160383600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:160382600-160383600	Weak transcription	Stomach Mucosa	stomach
13	chr3:160382800-160383000	Weak transcription	GM12878-XiMat	blood
14	chr3:160382800-160384200	Enhancers	Fetal Thymus	thymus

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