Variant report

Variant	rs56198248
Chromosome Location	chr16:81108474-81108475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81096522..81104265-chr16:81107324..81112531,10	MCF-7	breast:
2	chr16:81039722..81044457-chr16:81106699..81112118,5	MCF-7	breast:
3	chr16:81038376..81043277-chr16:81108432..81112403,6	K562	blood:
4	chr16:81038376..81042418-chr16:81108432..81111584,4	K562	blood:
5	chr16:81101883..81103622-chr16:81105773..81108523,2	K562	blood:
6	chr16:81039624..81041255-chr16:81107979..81110813,2	MCF-7	breast:
7	chr16:81067084..81072191-chr16:81106033..81112629,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000261838	Chromatin interaction
ENSG00000103121	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1035541	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10459871	0.90[AFR][1000 genomes]
rs10459872	0.90[AFR][1000 genomes]
rs1048194	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050364	0.91[EUR][1000 genomes]
rs10514512	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10514513	0.91[EUR][1000 genomes]
rs10514514	0.91[EUR][1000 genomes]
rs10514515	0.91[EUR][1000 genomes]
rs11866124	0.85[EUR][1000 genomes]
rs12443549	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12444137	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12444747	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444969	0.84[AFR][1000 genomes]
rs12444974	0.82[EUR][1000 genomes]
rs12445303	0.91[EUR][1000 genomes]
rs12448806	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12456	0.87[EUR][1000 genomes]
rs12598621	0.91[EUR][1000 genomes]
rs1410	0.87[EUR][1000 genomes]
rs1412	0.89[EUR][1000 genomes]
rs1414	0.89[EUR][1000 genomes]
rs1563072	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563075	0.94[EUR][1000 genomes]
rs1563077	0.91[EUR][1000 genomes]
rs16954513	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954572	0.91[EUR][1000 genomes]
rs16954582	0.91[EUR][1000 genomes]
rs1814543	0.82[EUR][1000 genomes]
rs2278024	0.81[EUR][1000 genomes]
rs2316730	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2316731	0.84[EUR][1000 genomes]
rs2317085	0.87[EUR][1000 genomes]
rs2317086	0.86[EUR][1000 genomes]
rs2317087	0.95[EUR][1000 genomes]
rs28391685	0.91[EUR][1000 genomes]
rs28613188	0.91[EUR][1000 genomes]
rs28672349	0.91[EUR][1000 genomes]
rs4306521	0.91[EUR][1000 genomes]
rs4324141	0.91[EUR][1000 genomes]
rs4324142	0.91[EUR][1000 genomes]
rs4324143	0.91[EUR][1000 genomes]
rs4454990	0.87[EUR][1000 genomes]
rs4889225	0.80[EUR][1000 genomes]
rs4889227	0.91[EUR][1000 genomes]
rs4889229	0.80[EUR][1000 genomes]
rs4889230	0.80[EUR][1000 genomes]
rs4889231	0.91[EUR][1000 genomes]
rs4889233	0.85[EUR][1000 genomes]
rs5023849	0.85[EUR][1000 genomes]
rs5023850	0.82[EUR][1000 genomes]
rs5023852	0.85[EUR][1000 genomes]
rs55939311	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs56032321	0.91[EUR][1000 genomes]
rs56119129	0.91[EUR][1000 genomes]
rs56166222	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs56286107	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375210	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56395947	0.91[EUR][1000 genomes]
rs57606521	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58144189	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59177227	0.91[EUR][1000 genomes]
rs59685942	0.91[EUR][1000 genomes]
rs61082942	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6420419	0.85[EUR][1000 genomes]
rs6420421	0.85[EUR][1000 genomes]
rs7188508	0.91[EUR][1000 genomes]
rs7203546	0.80[EUR][1000 genomes]
rs7204040	0.91[EUR][1000 genomes]
rs7206814	0.80[EUR][1000 genomes]
rs73597252	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754429	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8043855	0.82[EUR][1000 genomes]
rs804895	0.82[EUR][1000 genomes]
rs804897	0.87[EUR][1000 genomes]
rs804902	0.80[EUR][1000 genomes]
rs8052490	0.91[EUR][1000 genomes]
rs8056972	0.91[EUR][1000 genomes]
rs8059692	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177851	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177876	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177939	0.88[EUR][1000 genomes]
rs8177940	0.91[EUR][1000 genomes]
rs8177942	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs8177943	0.91[EUR][1000 genomes]
rs8177945	0.89[EUR][1000 genomes]
rs8177948	0.91[EUR][1000 genomes]
rs8177950	0.91[EUR][1000 genomes]
rs8177959	0.89[EUR][1000 genomes]
rs874437	0.97[EUR][1000 genomes]
rs935942	0.80[EUR][1000 genomes]
rs9923732	0.91[EUR][1000 genomes]
rs9925940	0.91[EUR][1000 genomes]
rs9925943	0.91[EUR][1000 genomes]
rs9926174	0.91[EUR][1000 genomes]
rs9929586	0.91[EUR][1000 genomes]
rs9933184	0.91[EUR][1000 genomes]
rs9938965	0.91[EUR][1000 genomes]

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	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs56198248	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs56198248	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs56198248	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs56198248	GCSH	cis	Muscle Skeletal	GTEx
rs56198248	C16orf46	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81079400-81109800	Weak transcription	Brain Hippocampus Middle	brain
2	chr16:81080400-81110200	Weak transcription	Ovary	ovary
3	chr16:81093000-81109800	Weak transcription	Brain Anterior Caudate	brain
4	chr16:81095000-81109400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr16:81095600-81109800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:81095800-81110200	Weak transcription	Fetal Stomach	stomach
7	chr16:81101000-81110000	Weak transcription	Fetal Brain Male	brain
8	chr16:81102000-81109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:81105600-81109400	Weak transcription	Fetal Heart	heart
10	chr16:81105800-81109400	Weak transcription	Hela-S3	cervix
11	chr16:81105800-81109600	Weak transcription	HepG2	liver
12	chr16:81105800-81109800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:81105800-81109800	Weak transcription	HMEC	breast
14	chr16:81105800-81109800	Weak transcription	NHEK	skin
15	chr16:81105800-81110000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:81105800-81110000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr16:81105800-81110000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr16:81106000-81109400	Weak transcription	K562	blood
19	chr16:81106000-81109800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr16:81106600-81110200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:81107200-81109800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr16:81107400-81109800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:81107600-81109600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr16:81107600-81109800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:81107600-81109800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr16:81107600-81109800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr16:81107600-81110200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr16:81107800-81109800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr16:81107800-81109800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr16:81107800-81109800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr16:81107800-81110000	Enhancers	Placenta	Placenta
32	chr16:81108000-81110000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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