Variant report

Variant	rs4889233
Chromosome Location	chr16:81126983-81126984
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81109242..81112738-chr16:81125910..81131139,12	MCF-7	breast:
2	chr16:81109109..81111856-chr16:81126620..81130593,5	MCF-7	breast:
3	chr16:81109367..81115509-chr16:81122988..81128884,9	K562	blood:
4	chr16:81039840..81042358-chr16:81124193..81127113,2	K562	blood:
5	chr16:81112617..81114172-chr16:81125649..81127848,2	K562	blood:
6	chr16:81125930..81127449-chr16:81128575..81130683,2	MCF-7	breast:
7	chr16:81068173..81071730-chr16:81126382..81131671,6	MCF-7	breast:
8	chr16:81125448..81127005-chr16:81128655..81130332,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245059	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000140905	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000260213	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10459871	0.90[CEU][hapmap]
rs10459872	0.90[CEU][hapmap]
rs1048194	0.80[CEU][hapmap]
rs10514512	0.90[CEU][hapmap]
rs10514513	0.90[CEU][hapmap]
rs10514514	0.90[CEU][hapmap]
rs10514515	0.90[CEU][hapmap]
rs11150337	0.81[EUR][1000 genomes]
rs11537	0.90[CEU][hapmap]
rs11866124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443549	0.90[CEU][hapmap]
rs12444137	0.90[CEU][hapmap]
rs12444747	0.80[CEU][hapmap]
rs12444974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445303	0.90[CEU][hapmap]
rs12448806	0.83[EUR][1000 genomes]
rs12456	0.80[CEU][hapmap]
rs12918103	1.00[CHB][hapmap]
rs12919980	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12921900	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12921990	0.97[ASN][1000 genomes]
rs12922449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12927239	0.80[CEU][hapmap]
rs12928381	1.00[CHB][hapmap]
rs12928648	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12928790	0.97[ASN][1000 genomes]
rs12929250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12930202	1.00[CHB][hapmap]
rs12931678	1.00[CHB][hapmap]
rs12932466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13185	0.81[CEU][hapmap]
rs1414	0.90[CEU][hapmap]
rs1563072	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1563075	0.90[CEU][hapmap]
rs16954505	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs16954513	0.80[CEU][hapmap]
rs16954572	0.90[CEU][hapmap]
rs16954582	0.90[CEU][hapmap]
rs2278021	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2278022	0.80[CEU][hapmap]
rs2278023	1.00[CHB][hapmap]
rs2278024	0.88[CEU][hapmap]
rs2303214	1.00[CHB][hapmap]
rs2316730	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs2317087	0.83[EUR][1000 genomes]
rs2549891	0.89[CEU][hapmap]
rs2549893	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2549896	0.90[CEU][hapmap]
rs2602402	0.90[CEU][hapmap]
rs2602407	0.90[CEU][hapmap]
rs2970076	0.90[CEU][hapmap]
rs2970077	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs34270219	0.97[ASN][1000 genomes]
rs35161190	0.82[ASN][1000 genomes]
rs35887664	0.84[ASN][1000 genomes]
rs36052656	0.97[ASN][1000 genomes]
rs4324141	0.90[CEU][hapmap]
rs4454990	0.80[CEU][hapmap]
rs4889225	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs4889229	0.89[EUR][1000 genomes]
rs4889230	0.89[EUR][1000 genomes]
rs5023849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5023850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5023852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56198248	0.85[EUR][1000 genomes]
rs56286107	0.83[EUR][1000 genomes]
rs59022620	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60303302	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6420419	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6420421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564819	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7185637	0.90[EUR][1000 genomes]
rs7203546	0.89[EUR][1000 genomes]
rs7204040	0.90[CEU][hapmap]
rs7206814	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs73597252	0.88[EUR][1000 genomes]
rs754429	0.90[CEU][hapmap]
rs8043855	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8047495	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs804885	0.90[CEU][hapmap]
rs804895	0.81[CEU][hapmap]
rs804902	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs8050720	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8052415	0.81[EUR][1000 genomes]
rs8052490	0.90[CEU][hapmap]
rs8052694	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8056972	0.90[CEU][hapmap]
rs8059692	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs8177849	0.97[ASN][1000 genomes]
rs8177851	0.85[EUR][1000 genomes]
rs8177862	0.97[ASN][1000 genomes]
rs8177863	0.97[ASN][1000 genomes]
rs8177876	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs8177878	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs8177891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8177919	0.87[ASN][1000 genomes]
rs8177938	0.84[ASN][1000 genomes]
rs8177940	0.85[CEU][hapmap]
rs8177957	0.90[CEU][hapmap]
rs8177959	0.90[CEU][hapmap]
rs874437	0.88[EUR][1000 genomes]
rs935942	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs9923732	0.85[CEU][hapmap]
rs9925940	0.90[CEU][hapmap]
rs9925943	0.90[CEU][hapmap]
rs9926174	0.90[CEU][hapmap]
rs9929586	0.90[CEU][hapmap]
rs9933184	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4889233	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs4889233	GCSH	cis	Muscle Skeletal	GTEx
rs4889233	ATMIN	cis	Muscle Skeletal	GTEx
rs4889233	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs4889233	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs4889233	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81111400-81128200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr16:81111400-81128400	Weak transcription	Aorta	Aorta
3	chr16:81111400-81128800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:81111400-81128800	Weak transcription	Psoas Muscle	Psoas
5	chr16:81111400-81128800	Weak transcription	NHDF-Ad	bronchial
6	chr16:81111400-81129000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:81111400-81129000	Weak transcription	Gastric	stomach
8	chr16:81111400-81129200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr16:81111600-81127800	Weak transcription	Brain Substantia Nigra	brain
10	chr16:81111600-81128000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr16:81111600-81128200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:81111600-81128200	Weak transcription	Brain Hippocampus Middle	brain
13	chr16:81111600-81128200	Weak transcription	NH-A	brain
14	chr16:81111600-81128400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:81111600-81128400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:81111600-81128400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr16:81111600-81128400	Weak transcription	Brain Anterior Caudate	brain
18	chr16:81111600-81128400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr16:81111600-81128400	Weak transcription	HSMM	muscle
20	chr16:81111600-81128600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:81111600-81128600	Weak transcription	Fetal Kidney	kidney
22	chr16:81111600-81128600	Weak transcription	Pancreas	Pancrea
23	chr16:81111600-81128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr16:81111600-81128800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:81111600-81128800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr16:81111600-81128800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr16:81111600-81128800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr16:81111600-81128800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr16:81111600-81128800	Weak transcription	Colon Smooth Muscle	Colon
30	chr16:81111600-81128800	Weak transcription	Fetal Brain Female	brain
31	chr16:81111600-81128800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr16:81111600-81128800	Weak transcription	Right Atrium	heart
33	chr16:81111600-81128800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr16:81111600-81128800	Weak transcription	HSMMtube	muscle
35	chr16:81111600-81128800	Weak transcription	Osteobl	bone
36	chr16:81111600-81129000	Weak transcription	Brain Germinal Matrix	brain
37	chr16:81111600-81129000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr16:81111600-81129200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr16:81111600-81129200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr16:81111600-81129200	Weak transcription	Left Ventricle	heart
41	chr16:81111800-81128200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr16:81111800-81128200	Weak transcription	Primary B cells from cord blood	blood
43	chr16:81111800-81128800	Weak transcription	Fetal Brain Male	brain
44	chr16:81111800-81128800	Weak transcription	Fetal Thymus	thymus
45	chr16:81113800-81127400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr16:81114000-81128400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:81114800-81127400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:81115200-81127200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr16:81117600-81128200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr16:81118000-81128000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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