Variant report

Variant	rs2443079
Chromosome Location	chr5:90110224-90110225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90105553..90108677-chr5:90109621..90112137,3	MCF-7	breast:
2	chr5:90108587..90111561-chr5:90677135..90678808,2	K562	blood:
3	chr5:89704530..89707367-chr5:90108211..90111116,2	K562	blood:
4	chr5:90106148..90108650-chr5:90109750..90111841,2	K562	blood:
5	chr5:90100827..90103086-chr5:90108487..90111195,2	K562	blood:
6	chr5:90100538..90103086-chr5:90108487..90111005,2	K562	blood:

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12519770	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13188479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2244356	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247546	0.81[ASN][1000 genomes]
rs2247870	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2438352	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2438353	0.89[CEU][hapmap]
rs2438355	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs2438362	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2438364	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2438368	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2443085	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2443091	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2460167	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs7720206	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2443079	GPR98	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90092400-90122200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:90098000-90111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:90098800-90111400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:90099000-90112200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:90100600-90119200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:90101200-90111200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:90102200-90113600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:90103000-90140800	Weak transcription	Brain Germinal Matrix	brain
9	chr5:90103600-90112200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:90104600-90142000	Weak transcription	Brain Anterior Caudate	brain
11	chr5:90106000-90117800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:90106800-90111600	Weak transcription	Fetal Brain Female	brain
13	chr5:90106800-90128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:90107000-90111400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:90107000-90111400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:90107200-90111400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:90108800-90111400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:90109000-90111400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:90109200-90111600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:90109600-90110600	Weak transcription	K562	blood
21	chr5:90109800-90112200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:90110200-90149600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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