Variant report

Variant	rs9630729
Chromosome Location	chr17:38807861-38807862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38804043..38806007-chr17:38806037..38808129,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11078950	0.89[EUR][1000 genomes]
rs11650910	0.89[EUR][1000 genomes]
rs11654834	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11659024	0.88[ASN][1000 genomes]
rs11869540	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474454	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1526601	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16966093	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961204	0.81[EUR][1000 genomes]
rs2011870	0.88[EUR][1000 genomes]
rs2429547	0.87[EUR][1000 genomes]
rs2429548	0.89[EUR][1000 genomes]
rs2429550	0.81[EUR][1000 genomes]
rs2429551	0.81[EUR][1000 genomes]
rs2462957	0.85[EUR][1000 genomes]
rs2462960	0.86[EUR][1000 genomes]
rs2462961	0.88[EUR][1000 genomes]
rs2462965	0.80[EUR][1000 genomes]
rs2462966	0.81[EUR][1000 genomes]
rs2469817	0.81[EUR][1000 genomes]
rs2469820	0.81[EUR][1000 genomes]
rs2469825	0.89[EUR][1000 genomes]
rs55664118	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6503545	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6503546	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67138687	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7224919	0.90[ASN][1000 genomes]
rs8065040	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8066541	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8074179	0.87[ASN][1000 genomes]
rs8074758	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs874889	0.84[EUR][1000 genomes]
rs887376	0.84[EUR][1000 genomes]
rs9303294	0.87[EUR][1000 genomes]
rs9894823	0.86[ASN][1000 genomes]
rs9902509	0.88[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	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9630729	SMARCE1	cis	multi-tissue	Pritchard
rs9630729	KRT24	cis	Esophagus Mucosa	GTEx
rs9630729	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs9630729	CCR7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38805200-38815800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:38805400-38808800	Weak transcription	NHLF	lung
3	chr17:38805400-38809400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:38805400-38812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:38805400-38816000	Weak transcription	Primary T cells from cord blood	blood
6	chr17:38805400-38821200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:38805600-38808200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:38805600-38809200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:38805600-38809400	Weak transcription	NHEK	skin
10	chr17:38805600-38815800	Weak transcription	Liver	Liver
11	chr17:38805600-38819400	Weak transcription	Spleen	Spleen
12	chr17:38805600-38820600	Weak transcription	Brain Anterior Caudate	brain
13	chr17:38805600-38821000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:38806200-38808200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:38806200-38809200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:38806200-38812600	Weak transcription	Fetal Muscle Leg	muscle
17	chr17:38806400-38809200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:38807400-38808400	Enhancers	Fetal Intestine Small	intestine
19	chr17:38807400-38808800	Enhancers	K562	blood

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