Variant report

Variant	rs1651654
Chromosome Location	chr16:46856589-46856590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:46856407..46858707-chr16:46862664..46865192,2	K562	blood:
2	chr16:46852133..46853769-chr16:46855489..46857597,2	K562	blood:
3	chr16:46855816..46858578-chr16:46865585..46867919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155330	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1009391	1.00[GIH][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs10468399	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11860484	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1641121	0.83[EUR][1000 genomes]
rs1641122	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs166161	0.84[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs16948661	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189741	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]
rs17792604	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs183672	1.00[ASN][1000 genomes]
rs1869006	1.00[GIH][hapmap];0.83[TSI][hapmap]
rs2341041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs252721	1.00[ASN][1000 genomes]
rs252722	1.00[ASN][1000 genomes]
rs28174	1.00[ASN][1000 genomes]
rs28184	1.00[ASN][1000 genomes]
rs28485103	1.00[ASN][1000 genomes]
rs35444809	1.00[ASN][1000 genomes]
rs36310	0.86[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs36312	1.00[ASN][1000 genomes]
rs36462	1.00[ASN][1000 genomes]
rs36464	1.00[ASN][1000 genomes]
rs36471	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs36476	1.00[ASN][1000 genomes]
rs36481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36483	1.00[ASN][1000 genomes]
rs40163	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs40355	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs41187	0.86[CEU][hapmap];1.00[CHD][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs4141491	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs415018	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420865	1.00[ASN][1000 genomes]
rs42461	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4401068	0.86[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966606	1.00[ASN][1000 genomes]
rs4966616	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4966708	1.00[GIH][hapmap]
rs4966713	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs4967393	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs4967576	0.80[EUR][1000 genomes]
rs4967602	1.00[GIH][hapmap]
rs4967621	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs57942848	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59064826	1.00[ASN][1000 genomes]
rs60500837	1.00[ASN][1000 genomes]
rs62057633	0.80[EUR][1000 genomes]
rs66508669	1.00[ASN][1000 genomes]
rs66804065	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67506574	1.00[ASN][1000 genomes]
rs67611436	1.00[ASN][1000 genomes]
rs67789219	1.00[ASN][1000 genomes]
rs68074363	1.00[ASN][1000 genomes]
rs68162608	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698418	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs700582	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs712816	1.00[ASN][1000 genomes]
rs7186662	1.00[ASN][1000 genomes]
rs7187475	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190713	1.00[ASN][1000 genomes]
rs7197033	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197485	0.90[GIH][hapmap]
rs7198951	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7205668	1.00[ASN][1000 genomes]
rs72816835	1.00[ASN][1000 genomes]
rs72816877	1.00[ASN][1000 genomes]
rs734309	0.89[GIH][hapmap]
rs794279	0.86[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs8044443	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8044684	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs8045353	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046748	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs8051017	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]
rs8053297	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8058734	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs808432	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs808434	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808780	0.93[CEU][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808783	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328668	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[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	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
9	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
10	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
11	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
12	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
13	esv3351528	chr16:46853500-46877470	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1651654	SHCBP1	cis	parietal	SCAN
rs1651654	LONP2	cis	cerebellum	SCAN
rs1651654	MYLK3	cis	cerebellum	SCAN
rs1651654	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46824600-46863800	Weak transcription	Aorta	Aorta
2	chr16:46829000-46863400	Weak transcription	Fetal Stomach	stomach
3	chr16:46829600-46857600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:46829600-46860000	Weak transcription	Fetal Brain Male	brain
5	chr16:46831600-46863000	Weak transcription	Fetal Muscle Leg	muscle
6	chr16:46831600-46863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr16:46833600-46863000	Weak transcription	Fetal Thymus	thymus
8	chr16:46833600-46864200	Weak transcription	Pancreas	Pancrea
9	chr16:46834200-46863800	Weak transcription	Placenta	Placenta
10	chr16:46834600-46863800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr16:46834800-46857600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr16:46835000-46862800	Weak transcription	HSMMtube	muscle
13	chr16:46836800-46863000	Weak transcription	Colon Smooth Muscle	Colon
14	chr16:46837000-46857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr16:46837000-46863000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:46840000-46857200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr16:46840200-46863800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:46841600-46863000	Weak transcription	Thymus	Thymus
19	chr16:46842000-46857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr16:46842400-46857600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr16:46844000-46860600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:46844200-46860200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:46844200-46862000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:46844200-46863200	Weak transcription	Adipose Nuclei	Adipose
25	chr16:46844400-46860200	Weak transcription	Fetal Lung	lung
26	chr16:46844400-46860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:46844600-46860200	Weak transcription	HUVEC	blood vessel
28	chr16:46845000-46860000	Weak transcription	HepG2	liver
29	chr16:46845200-46863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:46845200-46863400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr16:46848400-46864200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr16:46848600-46862400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:46849200-46860400	Weak transcription	Primary T cells from cord blood	blood
34	chr16:46849200-46862800	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:46849200-46863000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr16:46849800-46857600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr16:46849800-46859200	Weak transcription	Liver	Liver
38	chr16:46850000-46860200	Weak transcription	Brain Germinal Matrix	brain
39	chr16:46850000-46860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:46850400-46860000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr16:46851000-46856800	Weak transcription	Primary B cells from cord blood	blood
42	chr16:46851200-46857600	Weak transcription	Dnd41	blood
43	chr16:46851200-46858000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:46851200-46860400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr16:46852000-46860600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr16:46852200-46860600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr16:46852400-46860400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr16:46852400-46862400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr16:46852600-46859200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:46853800-46863000	Weak transcription	Fetal Intestine Small	intestine

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