Variant report

Variant	rs1466863
Chromosome Location	chr16:69904138-69904139
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69819983..69822871-chr16:69902631..69905244,2	K562	blood:

Variant related genes	Relation type
ENSG00000252443	Chromatin interaction
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10852460	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10852461	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11075742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075744	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs1116544	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11642008	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11645565	0.84[AMR][1000 genomes]
rs11648348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12598642	0.91[CHD][hapmap]
rs12927168	0.80[EUR][1000 genomes]
rs1500337	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[ASN][1000 genomes]
rs1566453	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1566454	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1566455	0.84[ASN][1000 genomes]
rs1566456	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2133799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291959	0.92[CHD][hapmap];0.83[MEX][hapmap]
rs2362642	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2937121	0.92[CHD][hapmap];0.83[MEX][hapmap]
rs3790075	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3790076	0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs3790080	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3790082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3790083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4146819	0.86[CHB][hapmap]
rs4985447	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985448	0.98[ASN][1000 genomes]
rs4985449	0.98[ASN][1000 genomes]
rs4985450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55887947	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499263	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6499265	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6499268	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6499269	0.87[ASN][1000 genomes]
rs6499270	0.86[CHB][hapmap];0.92[CHD][hapmap];0.87[MEX][hapmap]
rs7190013	0.98[ASN][1000 genomes]
rs7196842	0.86[CHB][hapmap];0.91[CHD][hapmap];0.83[MEX][hapmap]
rs7196917	0.86[AMR][1000 genomes]
rs7200005	0.96[MEX][hapmap]
rs7200258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7202233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73572177	0.85[ASN][1000 genomes]
rs8043925	0.83[ASW][hapmap];0.96[MEX][hapmap]
rs8047194	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8047682	0.94[ASN][1000 genomes]
rs8048550	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8049373	0.94[ASN][1000 genomes]
rs8050414	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8050516	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051168	0.86[ASN][1000 genomes]
rs8060478	0.94[ASN][1000 genomes]
rs8063226	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9927967	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9936589	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9936723	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9940315	0.92[CHD][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv960355	chr16:69901844-69907446	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1466863	LOC440348	cis	multi-tissue	Pritchard
rs1466863	LOC283970	cis	multi-tissue	Pritchard
rs1466863	MTSS1L	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69837000-69905600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69874000-69905800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:69876000-69904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:69876000-69905800	Weak transcription	Dnd41	blood
6	chr16:69876200-69905800	Weak transcription	Brain Germinal Matrix	brain
7	chr16:69883600-69904400	Weak transcription	HMEC	breast
8	chr16:69888000-69905600	Weak transcription	Gastric	stomach
9	chr16:69889600-69905600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:69890400-69923400	Weak transcription	HUVEC	blood vessel
11	chr16:69892600-69905400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:69893000-69906800	Weak transcription	GM12878-XiMat	blood
13	chr16:69893000-69907000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr16:69893000-69934800	Weak transcription	Hela-S3	cervix
15	chr16:69893200-69904600	Weak transcription	NHEK	skin
16	chr16:69893200-69906400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr16:69893200-69923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr16:69893400-69905000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr16:69893400-69906400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:69893600-69905600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:69893600-69910600	Weak transcription	A549	lung
22	chr16:69895200-69905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr16:69895400-69905600	Weak transcription	Aorta	Aorta
24	chr16:69895600-69906200	Weak transcription	Fetal Brain Female	brain
25	chr16:69895800-69907000	Weak transcription	Small Intestine	intestine
26	chr16:69896000-69905600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:69896000-69905800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr16:69896000-69906200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr16:69896000-69906400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr16:69896000-69906400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr16:69896000-69909400	Weak transcription	Fetal Kidney	kidney
32	chr16:69896200-69905000	Weak transcription	Brain Hippocampus Middle	brain
33	chr16:69896200-69905400	Weak transcription	Brain Angular Gyrus	brain
34	chr16:69896200-69905600	Weak transcription	Brain Anterior Caudate	brain
35	chr16:69896400-69905800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr16:69896400-69906600	Weak transcription	Stomach Mucosa	stomach
37	chr16:69896400-69910000	Weak transcription	Fetal Lung	lung
38	chr16:69896600-69904800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr16:69896600-69905400	Weak transcription	Brain Substantia Nigra	brain
40	chr16:69896600-69905600	Weak transcription	Adipose Nuclei	Adipose
41	chr16:69896600-69905600	Weak transcription	Lung	lung
42	chr16:69896600-69905600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr16:69896600-69905600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr16:69896600-69905600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr16:69896600-69906600	Weak transcription	Colon Smooth Muscle	Colon
46	chr16:69896600-69909200	Strong transcription	Fetal Intestine Small	intestine
47	chr16:69896600-69910200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr16:69896800-69905400	Weak transcription	Liver	Liver
49	chr16:69896800-69907200	Weak transcription	Right Atrium	heart
50	chr16:69897000-69905000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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