Variant report

Variant	rs17189741
Chromosome Location	chr16:46842785-46842786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46841434..46846391-chr16:46846846..46850783,4	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1009391	0.90[GIH][hapmap];0.85[TSI][hapmap]
rs10468399	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs1641122	0.84[EUR][1000 genomes]
rs1651654	0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166161	0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948661	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17792604	0.93[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183672	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs1869006	0.90[GIH][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs2341041	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252721	0.86[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs252722	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28174	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28184	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485103	1.00[ASN][1000 genomes]
rs35444809	1.00[ASN][1000 genomes]
rs36310	0.93[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs36312	1.00[ASN][1000 genomes]
rs36462	0.86[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36464	0.88[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36471	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36472	0.83[EUR][1000 genomes]
rs36476	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36481	0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36483	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40163	0.93[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40355	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41187	0.93[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141491	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415018	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420865	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42461	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4401068	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]
rs4966606	1.00[ASN][1000 genomes]
rs4966616	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4966708	0.88[GIH][hapmap]
rs4966713	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs4967393	0.93[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.90[GIH][hapmap]
rs4967621	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs57942848	0.85[EUR][1000 genomes]
rs59064826	1.00[ASN][1000 genomes]
rs60500837	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66508669	1.00[ASN][1000 genomes]
rs66804065	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205347	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67506574	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67611436	1.00[ASN][1000 genomes]
rs67789219	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68074363	1.00[ASN][1000 genomes]
rs68162608	0.85[EUR][1000 genomes]
rs698418	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700582	0.86[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712816	1.00[ASN][1000 genomes]
rs7186662	1.00[ASN][1000 genomes]
rs7187475	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190713	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197485	0.81[GIH][hapmap]
rs7198951	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205668	1.00[ASN][1000 genomes]
rs72816835	1.00[ASN][1000 genomes]
rs72816877	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794279	0.93[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044443	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs8044684	0.93[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045353	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046748	0.91[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051017	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	0.84[EUR][1000 genomes]
rs8058734	0.84[EUR][1000 genomes]
rs808432	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs808434	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808780	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808783	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328668	0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv1067283	chr16:46801709-46885218	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	esv1797464	chr16:46820464-46857454	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17189741	LONP2	cis	cerebellum	SCAN
rs17189741	MYLK3	cis	cerebellum	SCAN
rs17189741	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs17189741	SHCBP1	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46824400-46846800	Weak transcription	Left Ventricle	heart
2	chr16:46824400-46847200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:46824600-46843200	Weak transcription	HUVEC	blood vessel
4	chr16:46824600-46843600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr16:46824600-46843800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr16:46824600-46856000	Weak transcription	Ovary	ovary
7	chr16:46824600-46863800	Weak transcription	Aorta	Aorta
8	chr16:46824800-46843400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr16:46824800-46843600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:46824800-46843600	Weak transcription	NH-A	brain
11	chr16:46824800-46843600	Weak transcription	Osteobl	bone
12	chr16:46825000-46855200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr16:46825400-46843400	Weak transcription	K562	blood
14	chr16:46829000-46843200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr16:46829000-46855000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr16:46829000-46863400	Weak transcription	Fetal Stomach	stomach
17	chr16:46829200-46843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:46829200-46843400	Weak transcription	A549	lung
19	chr16:46829600-46857600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr16:46829600-46860000	Weak transcription	Fetal Brain Male	brain
21	chr16:46831000-46843400	Weak transcription	Fetal Kidney	kidney
22	chr16:46831200-46843600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:46831200-46843600	Weak transcription	Adipose Nuclei	Adipose
24	chr16:46831200-46843600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr16:46831600-46843200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr16:46831600-46843400	Weak transcription	Fetal Intestine Small	intestine
27	chr16:46831600-46854600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:46831600-46863000	Weak transcription	Fetal Muscle Leg	muscle
29	chr16:46831600-46863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:46831800-46843400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr16:46832600-46843600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr16:46832800-46856000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr16:46833600-46863000	Weak transcription	Fetal Thymus	thymus
34	chr16:46833600-46864200	Weak transcription	Pancreas	Pancrea
35	chr16:46834200-46845000	Weak transcription	Fetal Brain Female	brain
36	chr16:46834200-46863800	Weak transcription	Placenta	Placenta
37	chr16:46834600-46863800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr16:46834800-46854600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr16:46834800-46857600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr16:46835000-46855200	Weak transcription	Psoas Muscle	Psoas
41	chr16:46835000-46862800	Weak transcription	HSMMtube	muscle
42	chr16:46835600-46843800	Weak transcription	Stomach Mucosa	stomach
43	chr16:46835800-46843400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:46836400-46843000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr16:46836800-46843400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr16:46836800-46845200	Weak transcription	Esophagus	oesophagus
47	chr16:46836800-46848800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:46836800-46863000	Weak transcription	Colon Smooth Muscle	Colon
49	chr16:46837000-46842800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr16:46837000-46843400	Weak transcription	Fetal Lung	lung

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