Variant report

Variant	rs17572843
Chromosome Location	chr5:90350227-90350228
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90344675..90347461-chr5:90349774..90351830,2	MCF-7	breast:
2	chr5:90349608..90351637-chr5:90352105..90354581,2	MCF-7	breast:
3	chr5:90348024..90350979-chr5:90676084..90679046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10074525	1.00[ASN][1000 genomes]
rs10514342	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs10514343	1.00[CEU][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738573	1.00[ASN][1000 genomes]
rs11743775	1.00[ASN][1000 genomes]
rs11744033	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs11744325	1.00[ASN][1000 genomes]
rs11949884	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs11951675	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs11952993	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955946	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186968	1.00[ASN][1000 genomes]
rs12187656	1.00[ASN][1000 genomes]
rs12187790	1.00[ASN][1000 genomes]
rs12188068	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188094	1.00[ASN][1000 genomes]
rs12188249	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188655	1.00[ASN][1000 genomes]
rs12189005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658697	0.94[YRI][hapmap]
rs13152882	0.94[YRI][hapmap]
rs17571029	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs17633498	1.00[ASN][1000 genomes]
rs1976566	1.00[ASN][1000 genomes]
rs2438348	1.00[ASN][1000 genomes]
rs3114653	1.00[ASN][1000 genomes]
rs34243354	1.00[ASN][1000 genomes]
rs34381536	1.00[ASN][1000 genomes]
rs35060258	1.00[ASN][1000 genomes]
rs35299092	1.00[ASN][1000 genomes]
rs3850657	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55792004	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55941525	1.00[ASN][1000 genomes]
rs56051320	1.00[ASN][1000 genomes]
rs56099704	1.00[ASN][1000 genomes]
rs56106025	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258383	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374052	1.00[ASN][1000 genomes]
rs62376462	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376463	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376491	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452927	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs66509877	1.00[ASN][1000 genomes]
rs6860216	1.00[ASN][1000 genomes]
rs6861614	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6880626	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886773	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs6888672	1.00[ASN][1000 genomes]
rs6888979	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889138	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72784617	1.00[ASN][1000 genomes]
rs72784624	1.00[ASN][1000 genomes]
rs72784689	1.00[ASN][1000 genomes]
rs72784700	1.00[ASN][1000 genomes]
rs72784702	1.00[ASN][1000 genomes]
rs73771166	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7711168	1.00[ASN][1000 genomes]
rs7721862	1.00[ASN][1000 genomes]
rs7723305	1.00[ASN][1000 genomes]
rs949789	1.00[ASN][1000 genomes]
rs951948	0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17572843	GPR98	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:90341200-90376600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:90344400-90353800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:90344800-90368000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:90348200-90350800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:90348200-90351000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:90348400-90350400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:90348400-90351600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr5:90349400-90354000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:90349600-90354000	Weak transcription	Fetal Intestine Large	intestine
11	chr5:90349600-90354000	Weak transcription	A549	lung
12	chr5:90349600-90358400	Weak transcription	Fetal Kidney	kidney
13	chr5:90349800-90350400	Enhancers	Primary hematopoietic stem cells	blood
14	chr5:90349800-90350600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:90349800-90350600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:90349800-90353800	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:90349800-90354000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:90349800-90354200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:90350000-90350400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr5:90350000-90354000	Weak transcription	Rectal Smooth Muscle	rectum

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