Variant report

Variant	rs1009391
Chromosome Location	chr16:46889354-46889355
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46888367..46890662-chr16:46962617..46964242,2	MCF-7	breast:
2	chr16:46882446..46885231-chr16:46887367..46889893,2	K562	blood:

Variant related genes	Relation type
ENSG00000261725	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10468399	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs11860484	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934580	1.00[ASN][1000 genomes]
rs12935606	0.85[EUR][1000 genomes]
rs1641122	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651654	1.00[GIH][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs166161	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs16948661	1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs17189741	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs1869006	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341041	0.80[EUR][1000 genomes]
rs2341043	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354454	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36310	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs36471	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs36481	1.00[GIH][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs40355	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs41187	0.81[TSI][hapmap]
rs4141491	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs4246381	0.85[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401068	0.90[GIH][hapmap]
rs4966616	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4966706	1.00[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	0.86[CEU][hapmap];1.00[GIH][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.85[EUR][1000 genomes]
rs56042735	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.84[EUR][1000 genomes]
rs57127559	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58074838	0.82[EUR][1000 genomes]
rs59708508	0.81[EUR][1000 genomes]
rs62057633	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66804065	0.80[EUR][1000 genomes]
rs67205347	0.80[EUR][1000 genomes]
rs67211229	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700582	0.82[GIH][hapmap]
rs7186748	0.85[EUR][1000 genomes]
rs7187475	1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs7192574	0.81[EUR][1000 genomes]
rs7196375	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs7197485	0.86[CEU][hapmap];0.90[GIH][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734309	0.89[GIH][hapmap]
rs794279	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs8044443	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045353	0.80[EUR][1000 genomes]
rs8051017	1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs8053137	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058734	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808432	0.86[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808434	0.80[EUR][1000 genomes]
rs808783	0.90[GIH][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap]
rs9328668	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1795793	chr16:46882046-46904119	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1009391	MYLK3	cis	cerebellum	SCAN
rs1009391	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs1009391	SHCBP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46883200-46890000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:46886200-46891200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr16:46886200-46891200	Weak transcription	Placenta	Placenta
4	chr16:46886200-46905600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:46886400-46893400	Weak transcription	Gastric	stomach
6	chr16:46887200-46891400	Weak transcription	Fetal Kidney	kidney
7	chr16:46887600-46896800	Enhancers	HepG2	liver
8	chr16:46888400-46891000	Weak transcription	Brain Hippocampus Middle	brain
9	chr16:46888400-46891000	Weak transcription	Brain Substantia Nigra	brain
10	chr16:46888400-46891200	Weak transcription	Brain Angular Gyrus	brain
11	chr16:46888400-46891200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr16:46888400-46891200	Weak transcription	Fetal Muscle Leg	muscle
13	chr16:46888400-46891200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr16:46888400-46896600	Weak transcription	Pancreas	Pancrea
15	chr16:46888400-46913400	Weak transcription	Esophagus	oesophagus
16	chr16:46888600-46891000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr16:46888600-46891000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:46888600-46891200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:46888600-46891200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr16:46888600-46891600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:46889200-46890600	Enhancers	Stomach Mucosa	stomach

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