Variant report

Variant	rs16948661
Chromosome Location	chr16:46848522-46848523
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: 93 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1009391	1.00[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][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	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1651654	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]
rs166161	0.84[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs17189741	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	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs183672	1.00[ASN][1000 genomes]
rs1869006	1.00[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]
rs2341041	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	0.84[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[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[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	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420865	1.00[ASN][1000 genomes]
rs42461	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4401068	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]
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];0.81[YRI][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	0.93[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205347	1.00[AFR][1000 genomes];1.00[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	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs698418	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[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190713	1.00[ASN][1000 genomes]
rs7197033	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197485	0.90[GIH][hapmap]
rs7198951	0.82[AMR][1000 genomes];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];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8044684	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs8045353	0.99[AFR][1000 genomes];1.00[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8058734	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs808432	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs808434	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808780	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808783	0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.85[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:12 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16948661	SHCBP1	cis	parietal	SCAN
rs16948661	LONP2	cis	cerebellum	SCAN
rs16948661	LOC388272	Cis_1M	lymphoblastoid	RTeQTL
rs16948661	MYLK3	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46824600-46856000	Weak transcription	Ovary	ovary
2	chr16:46824600-46863800	Weak transcription	Aorta	Aorta
3	chr16:46825000-46855200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr16:46829000-46855000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:46829000-46863400	Weak transcription	Fetal Stomach	stomach
6	chr16:46829600-46857600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:46829600-46860000	Weak transcription	Fetal Brain Male	brain
8	chr16:46831600-46854600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:46831600-46863000	Weak transcription	Fetal Muscle Leg	muscle
10	chr16:46831600-46863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:46832800-46856000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr16:46833600-46863000	Weak transcription	Fetal Thymus	thymus
13	chr16:46833600-46864200	Weak transcription	Pancreas	Pancrea
14	chr16:46834200-46863800	Weak transcription	Placenta	Placenta
15	chr16:46834600-46863800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:46834800-46854600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr16:46834800-46857600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:46835000-46855200	Weak transcription	Psoas Muscle	Psoas
19	chr16:46835000-46862800	Weak transcription	HSMMtube	muscle
20	chr16:46836800-46848800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr16:46836800-46863000	Weak transcription	Colon Smooth Muscle	Colon
22	chr16:46837000-46854800	Weak transcription	Fetal Intestine Large	intestine
23	chr16:46837000-46857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:46837000-46863000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr16:46839600-46855800	Weak transcription	Small Intestine	intestine
26	chr16:46840000-46856000	Weak transcription	HSMM	muscle
27	chr16:46840000-46857200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr16:46840200-46863800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr16:46841600-46852600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr16:46841600-46863000	Weak transcription	Thymus	Thymus
31	chr16:46842000-46857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:46842400-46849000	Weak transcription	Dnd41	blood
33	chr16:46842400-46857600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:46844000-46849800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr16:46844000-46850600	Weak transcription	Primary B cells from cord blood	blood
36	chr16:46844000-46852600	Weak transcription	Fetal Intestine Small	intestine
37	chr16:46844000-46854400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr16:46844000-46860600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr16:46844200-46848600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr16:46844200-46848800	Weak transcription	Brain Hippocampus Middle	brain
41	chr16:46844200-46849600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr16:46844200-46850000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr16:46844200-46856200	Weak transcription	NH-A	brain
44	chr16:46844200-46860200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr16:46844200-46862000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:46844200-46863200	Weak transcription	Adipose Nuclei	Adipose
47	chr16:46844400-46848600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr16:46844400-46851800	Weak transcription	Osteobl	bone
49	chr16:46844400-46854600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr16:46844400-46856000	Weak transcription	Primary monocytes fromperipheralblood	blood

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