Variant report

Variant	rs1563072
Chromosome Location	chr16:81129416-81129417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81062101..81064821-chr16:81128185..81130104,2	MCF-7	breast:
2	chr16:81038922..81040878-chr16:81128552..81130305,2	MCF-7	breast:
3	chr16:81068545..81070466-chr16:81128738..81130368,2	K562	blood:
4	chr16:81040036..81041738-chr16:81128465..81130557,3	MCF-7	breast:
5	chr16:81109242..81112738-chr16:81125910..81131139,12	MCF-7	breast:
6	chr16:81128511..81130849-chr16:81169835..81172966,4	MCF-7	breast:
7	chr16:81109109..81111856-chr16:81126620..81130593,5	MCF-7	breast:
8	chr16:81129311..81129999-chr6:74230291..74231167,2	Hela-S3	cervix:
9	chr16:81123255..81125056-chr16:81127455..81129707,2	MCF-7	breast:
10	chr16:81108969..81114076-chr16:81128464..81132360,7	K562	blood:
11	chr16:81066967..81071215-chr16:81128766..81132498,3	MCF-7	breast:
12	chr16:81128119..81130536-chr16:81138830..81141315,2	K562	blood:
13	chr16:81068173..81071730-chr16:81126382..81131671,6	MCF-7	breast:
14	chr16:81068545..81070561-chr16:81128158..81130238,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000245059	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166473	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000261061	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000252608	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000166455	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1035541	0.83[EUR][1000 genomes]
rs10459871	0.90[CEU][hapmap]
rs10459872	0.90[CEU][hapmap]
rs1048194	0.80[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050364	0.88[EUR][1000 genomes]
rs10514512	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs10514513	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs10514514	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs10514515	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs11537	0.90[CEU][hapmap]
rs11866124	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12443549	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs12444137	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs12444747	0.80[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444974	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12445303	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs12448806	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12456	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs12598621	0.88[EUR][1000 genomes]
rs12927239	0.80[CEU][hapmap]
rs13185	0.81[CEU][hapmap]
rs1410	0.84[EUR][1000 genomes]
rs1412	0.86[EUR][1000 genomes]
rs1414	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1563075	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs1563077	0.88[EUR][1000 genomes]
rs16954505	0.80[CEU][hapmap]
rs16954513	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs16954572	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs16954582	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs1814543	0.82[EUR][1000 genomes]
rs2045039	0.82[YRI][hapmap]
rs2278022	0.80[CEU][hapmap]
rs2278024	0.88[CEU][hapmap]
rs2316730	0.80[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316731	0.84[EUR][1000 genomes]
rs2317085	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2317086	0.86[EUR][1000 genomes]
rs2317087	0.95[EUR][1000 genomes]
rs2549891	0.89[CEU][hapmap]
rs2549896	0.90[CEU][hapmap]
rs2602402	0.90[CEU][hapmap]
rs2602407	0.90[CEU][hapmap]
rs28391685	0.88[EUR][1000 genomes]
rs28613188	0.88[EUR][1000 genomes]
rs28672349	0.88[EUR][1000 genomes]
rs2970076	0.90[CEU][hapmap]
rs2970077	0.80[CEU][hapmap]
rs4306521	0.88[EUR][1000 genomes]
rs4324141	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs4324142	0.88[EUR][1000 genomes]
rs4324143	0.88[EUR][1000 genomes]
rs4454990	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs4889225	0.90[CEU][hapmap]
rs4889226	0.82[YRI][hapmap]
rs4889227	0.88[EUR][1000 genomes]
rs4889231	0.88[EUR][1000 genomes]
rs4889233	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5023849	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5023850	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5023852	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55939311	0.89[EUR][1000 genomes]
rs56032321	0.88[EUR][1000 genomes]
rs56119129	0.88[EUR][1000 genomes]
rs56166222	0.89[EUR][1000 genomes]
rs56198248	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56286107	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375210	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56395947	0.88[EUR][1000 genomes]
rs57606521	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59177227	0.88[EUR][1000 genomes]
rs59685942	0.88[EUR][1000 genomes]
rs60303302	0.82[EUR][1000 genomes]
rs61082942	0.88[EUR][1000 genomes]
rs6420419	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6420421	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6564819	0.82[EUR][1000 genomes]
rs7188508	0.88[EUR][1000 genomes]
rs7204040	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs7206814	0.90[CEU][hapmap]
rs73597252	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754429	0.90[CEU][hapmap]
rs8043855	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs8047495	0.80[EUR][1000 genomes]
rs804885	0.90[CEU][hapmap]
rs804895	0.81[CEU][hapmap]
rs804897	0.84[EUR][1000 genomes]
rs804902	0.90[CEU][hapmap]
rs8052490	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs8056972	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs8059692	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177851	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177876	0.87[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177939	0.84[EUR][1000 genomes]
rs8177940	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs8177942	0.89[EUR][1000 genomes]
rs8177943	0.88[EUR][1000 genomes]
rs8177945	0.86[EUR][1000 genomes]
rs8177948	0.88[EUR][1000 genomes]
rs8177950	0.88[EUR][1000 genomes]
rs8177957	0.90[CEU][hapmap]
rs8177959	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs874437	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs935942	0.90[CEU][hapmap]
rs9923732	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs9925940	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9925943	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9926174	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9929586	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9933184	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9935436	0.81[AFR][1000 genomes]
rs9938965	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription 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	49 gene(s)	inside rSNPs	diseases
5	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv530715	chr16:81117168-81252875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv907005	chr16:81121353-81194912	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1067144	chr16:81129298-81181641	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1563072	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs1563072	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs1563072	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs1563072	GCSH	cis	Muscle Skeletal	GTEx
rs1563072	GCSH	cis	multi-tissue	Pritchard
rs1563072	ATMIN	cis	Muscle Skeletal	GTEx
rs1563072	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81128000-81130400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr16:81128000-81130400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr16:81128200-81130200	Active TSS	NH-A	brain
4	chr16:81128200-81130400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr16:81128200-81130600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr16:81128400-81129600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:81128400-81130000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:81128400-81130200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr16:81128400-81130200	Active TSS	NHLF	lung
10	chr16:81128400-81130400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:81128400-81130400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr16:81128400-81130400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:81128400-81130400	Active TSS	Brain Anterior Caudate	brain
14	chr16:81128400-81130400	Active TSS	A549	lung
15	chr16:81128400-81130400	Active TSS	HSMM	muscle
16	chr16:81128400-81130600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr16:81128400-81130600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:81128400-81130600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr16:81128400-81130600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:81128600-81129600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr16:81128600-81130000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:81128600-81130000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr16:81128600-81130000	Active TSS	Pancreas	Pancrea
24	chr16:81128600-81130200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:81128600-81130200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr16:81128600-81130200	Active TSS	Muscle Satellite Cultured Cells	--
27	chr16:81128600-81130200	Active TSS	Adipose Nuclei	Adipose
28	chr16:81128600-81130200	Active TSS	Fetal Lung	lung
29	chr16:81128600-81130200	Active TSS	Hela-S3	cervix
30	chr16:81128600-81130200	Active TSS	K562	blood
31	chr16:81128600-81130400	Active TSS	Primary T cells from cord blood	blood
32	chr16:81128600-81130400	Active TSS	Brain Angular Gyrus	brain
33	chr16:81128600-81130400	Active TSS	Brain Cingulate Gyrus	brain
34	chr16:81128600-81130400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr16:81128600-81130400	Active TSS	Ovary	ovary
36	chr16:81128600-81130600	Active TSS	H1 Cell Line	embryonic stem cell
37	chr16:81128600-81130600	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr16:81128800-81129600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr16:81128800-81129800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr16:81128800-81129800	Active TSS	Fetal Brain Male	brain
41	chr16:81128800-81129800	Active TSS	Placenta	Placenta
42	chr16:81128800-81129800	Enhancers	Stomach Mucosa	stomach
43	chr16:81128800-81129800	Active TSS	GM12878-XiMat	blood
44	chr16:81128800-81130000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:81128800-81130000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr16:81128800-81130000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr16:81128800-81130000	Active TSS	Aorta	Aorta
48	chr16:81128800-81130000	Active TSS	Right Atrium	heart
49	chr16:81128800-81130200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr16:81128800-81130200	Active TSS	Stomach Smooth Muscle	stomach

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