Variant report

Variant	rs27201
Chromosome Location	chr5:89844438-89844439
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89703071..89706811-chr5:89843444..89846319,3	K562	blood:
2	chr5:89705126..89706810-chr5:89842410..89844887,2	MCF-7	breast:
3	chr5:89843926..89847301-chr5:89847464..89849372,3	K562	blood:
4	chr5:89842756..89845213-chr5:89939588..89942557,2	K562	blood:
5	chr5:89825681..89827224-chr5:89844315..89846523,2	K562	blood:
6	chr5:89703142..89707771-chr5:89841561..89845408,5	K562	blood:
7	chr5:89844169..89846312-chr5:89898402..89900420,2	K562	blood:
8	chr5:89768870..89770487-chr5:89842476..89844601,2	MCF-7	breast:
9	chr5:89843795..89845765-chr5:89848333..89850090,2	MCF-7	breast:
10	chr5:89824636..89834797-chr5:89838005..89846568,18	MCF-7	breast:
11	chr5:89824246..89828197-chr5:89842395..89845815,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10069050	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs149321	0.81[JPT][hapmap]
rs154568	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs154569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs154570	0.93[EUR][1000 genomes]
rs154572	0.89[EUR][1000 genomes]
rs154573	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1553545	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs1673381	0.81[JPT][hapmap]
rs171790	0.91[EUR][1000 genomes]
rs2366772	0.80[JPT][hapmap]
rs250366	0.81[JPT][hapmap]
rs250377	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs257847	0.81[JPT][hapmap]
rs257850	0.91[EUR][1000 genomes]
rs257851	0.90[EUR][1000 genomes]
rs2656957	0.91[EUR][1000 genomes]
rs27196	0.90[JPT][hapmap]
rs27197	0.81[JPT][hapmap]
rs37238	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs37239	0.86[EUR][1000 genomes]
rs37240	0.85[EUR][1000 genomes]
rs42467	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs43149	0.91[EUR][1000 genomes]
rs4588621	0.81[JPT][hapmap]
rs491082	0.91[EUR][1000 genomes]
rs5028525	0.81[JPT][hapmap]
rs511393	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs526806	0.92[EUR][1000 genomes]
rs556894	0.92[EUR][1000 genomes]
rs59159252	0.82[ASN][1000 genomes]
rs594990	0.93[EUR][1000 genomes]
rs599432	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs625135	0.84[CEU][hapmap]
rs649449	0.81[JPT][hapmap]
rs656679	0.81[JPT][hapmap]
rs679568	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs6884154	0.80[EUR][1000 genomes]
rs6892132	0.81[JPT][hapmap]
rs810974	0.91[EUR][1000 genomes]

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	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs27201	GPR98	cis	cerebellum	SCAN
rs27201	GPR98	cis	parietal	SCAN
rs27201	LYSMD3	cis	normal skin	skin_eQTL
rs27201	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89840400-89845200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:89840800-89845800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:89842200-89844600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:89842200-89844800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:89842800-89844600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr5:89843000-89844600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:89843400-89849600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:89843400-89852800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:89843400-89853200	Weak transcription	Brain Anterior Caudate	brain
10	chr5:89843600-89844600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:89843800-89844800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:89844200-89848000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:89844200-89853200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:89844200-89853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:89844400-89844600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:89844400-89844600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:89844400-89844600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr5:89844400-89844600	Bivalent Enhancer	A549	lung
19	chr5:89844400-89844800	Active TSS	K562	blood
20	chr5:89844400-89849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:89844400-89849600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:89844400-89849600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:89844400-89853200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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