Variant report

Variant	rs11859801
Chromosome Location	chr16:12143056-12143057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12141844..12143563-chr16:12144575..12146387,2	K562	blood:
2	chr16:12008162..12010269-chr16:12142729..12146819,3	K562	blood:
3	chr16:12070192..12071929-chr16:12142370..12144393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266163	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000260488	Chromatin interaction
ENSG00000234719	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11075042	0.96[ASN][1000 genomes]
rs11859105	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11859378	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11859602	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11859670	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11862031	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11863344	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11863772	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864775	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11865036	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865132	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11865547	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs168408	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257492	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2865105	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34321532	0.89[ASN][1000 genomes]
rs34701893	0.89[ASN][1000 genomes]
rs35106911	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3826097	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826098	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851006	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851007	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3862465	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459292	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55719789	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55788618	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55845335	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55933754	0.82[ASN][1000 genomes]
rs55995758	0.89[ASN][1000 genomes]
rs56166842	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56325311	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56363861	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62037727	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037728	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62037734	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037735	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62037736	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62037739	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62037740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62037741	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6498261	0.83[CHD][hapmap]
rs7184186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192463	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196418	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197059	1.00[CHD][hapmap]
rs7200173	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202235	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202328	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7202330	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202375	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784623	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72784632	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8044821	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8045202	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051298	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8052866	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8057116	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv977110	chr16:12123355-12146787	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11859801	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr16:12119200-12146400	Weak transcription	Fetal Lung	lung
4	chr16:12119600-12148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:12121400-12155000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:12122800-12144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr16:12124400-12156600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:12124800-12155000	Weak transcription	NH-A	brain
9	chr16:12126400-12150000	Weak transcription	Small Intestine	intestine
10	chr16:12130000-12153000	Weak transcription	Ovary	ovary
11	chr16:12131200-12144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:12131200-12153000	Weak transcription	Right Atrium	heart
13	chr16:12131200-12156600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr16:12131400-12148200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr16:12131400-12150800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr16:12131400-12150800	Weak transcription	HSMMtube	muscle
17	chr16:12131600-12154800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:12132000-12150200	Weak transcription	Osteobl	bone
19	chr16:12132800-12154600	Weak transcription	Hela-S3	cervix
20	chr16:12133000-12147400	Weak transcription	NHDF-Ad	bronchial
21	chr16:12133000-12148200	Weak transcription	Fetal Brain Female	brain
22	chr16:12133000-12152800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:12133000-12153600	Weak transcription	Fetal Kidney	kidney
24	chr16:12133800-12156400	Weak transcription	Stomach Mucosa	stomach
25	chr16:12134000-12145200	Weak transcription	Placenta	Placenta
26	chr16:12134200-12153000	Weak transcription	HepG2	liver
27	chr16:12136200-12151600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:12136400-12145200	Weak transcription	Fetal Intestine Large	intestine
29	chr16:12136400-12152600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr16:12136800-12144800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:12138400-12149800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr16:12138400-12156800	Weak transcription	Colon Smooth Muscle	Colon
33	chr16:12138800-12151800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr16:12139200-12151400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr16:12139400-12172600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:12139800-12144600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr16:12139800-12146600	Strong transcription	Liver	Liver
38	chr16:12140000-12144400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr16:12140000-12146200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr16:12140000-12151200	Strong transcription	Fetal Stomach	stomach
41	chr16:12140200-12144600	Strong transcription	Lung	lung
42	chr16:12140200-12146000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr16:12140200-12150400	Strong transcription	Adipose Nuclei	Adipose
44	chr16:12140400-12143200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr16:12140400-12144400	Strong transcription	Primary T cells from cord blood	blood
46	chr16:12140400-12146600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr16:12140400-12148800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr16:12140600-12144400	Strong transcription	Fetal Muscle Leg	muscle
49	chr16:12140600-12146600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr16:12140800-12144400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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