Variant report

Variant	rs4401068
Chromosome Location	chr16:46797168-46797169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr16:46796867-46797219	T-47D	breast:	n/a	n/a
2	CTCF	chr16:46797100-46797250	HUVEC	blood vessel:	n/a	chr16:46797121-46797131 chr16:46797133-46797151
3	GATA3	chr16:46796832-46797260	T-47D	breast:	n/a	chr16:46797230-46797240
4	GATA3	chr16:46796887-46797246	T-47D	breast:	n/a	chr16:46797230-46797240
5	FOXA1	chr16:46796872-46797217	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46720929..46723857-chr16:46796007..46798416,2	MCF-7	breast:

Variant related genes	Relation type
MYLK3	TF binding region
ENSG00000091651	Chromatin interaction
ENSG00000069329	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1009391	0.90[GIH][hapmap]
rs10468399	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.90[GIH][hapmap]
rs1651654	0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166161	0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948661	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189741	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17792604	0.86[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183672	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869006	0.90[GIH][hapmap];0.81[MKK][hapmap]
rs2341041	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252721	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252722	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28174	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28184	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485103	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35444809	1.00[ASN][1000 genomes]
rs36310	0.86[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36312	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36462	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36464	0.88[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36471	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36472	0.90[EUR][1000 genomes]
rs36476	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36481	0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36483	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40163	0.86[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40355	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41187	0.86[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141491	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415018	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420865	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42461	0.89[EUR][1000 genomes]
rs4966606	1.00[ASN][1000 genomes]
rs4966616	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4966708	0.88[GIH][hapmap]
rs4966713	0.90[GIH][hapmap]
rs4967393	0.86[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.90[GIH][hapmap]
rs4967621	0.90[GIH][hapmap]
rs59064826	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60500837	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66508669	1.00[ASN][1000 genomes]
rs66804065	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205347	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67506574	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67611436	1.00[ASN][1000 genomes]
rs67789219	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68074363	1.00[ASN][1000 genomes]
rs698418	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700582	1.00[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712816	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186662	1.00[CHD][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7187475	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190713	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs7197485	0.81[GIH][hapmap]
rs7198951	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205668	1.00[ASN][1000 genomes]
rs72816835	1.00[ASN][1000 genomes]
rs72816877	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794279	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044443	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs8044684	0.86[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045353	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046748	0.82[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051017	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808434	0.86[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808780	0.93[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808783	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328668	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1064289	chr16:46463770-46801977	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv916976	chr16:46505597-46801868	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1067038	chr16:46721805-46797514	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv1066472	chr16:46721805-46801769	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1065253	chr16:46721805-46824369	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1059049	chr16:46721805-46859239	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	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
16	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4401068	MYLK3	cis	cerebellum	SCAN
rs4401068	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs4401068	LONP2	cis	cerebellum	SCAN
rs4401068	SHCBP1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46777600-46798200	Weak transcription	Spleen	Spleen
2	chr16:46791000-46823400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:46792400-46797200	Active TSS	Right Atrium	heart
4	chr16:46792600-46811600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:46793000-46809600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr16:46793600-46798800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:46795200-46797200	Active TSS	Right Ventricle	heart
8	chr16:46795400-46797200	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr16:46796400-46797400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:46796400-46797400	Active TSS	Brain Anterior Caudate	brain
11	chr16:46796400-46797600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:46796400-46797600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:46796400-46797600	Enhancers	HMEC	breast
14	chr16:46796400-46797800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr16:46796600-46798000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr16:46796800-46797400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:46796800-46797600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr16:46797000-46797200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr16:46797000-46797200	Flanking Active TSS	Left Ventricle	heart
20	chr16:46797000-46797400	Enhancers	Fetal Heart	heart
21	chr16:46797000-46797400	Enhancers	Fetal Muscle Trunk	muscle
22	chr16:46797000-46797600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:46797000-46797600	Enhancers	Psoas Muscle	Psoas
24	chr16:46797000-46797600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr16:46797000-46797600	Enhancers	NHEK	skin
26	chr16:46797000-46798200	Enhancers	Fetal Muscle Leg	muscle

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