Variant report

Variant	rs10514343
Chromosome Location	chr5:90322671-90322672
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90322563..90325086-chr5:90674731..90677361,2	K562	blood:
2	chr5:90322115..90324122-chr5:90324503..90326685,2	MCF-7	breast:
3	chr5:90321904..90323771-chr5:90678316..90680092,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10074525	1.00[ASN][1000 genomes]
rs10514342	0.91[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738573	1.00[ASN][1000 genomes]
rs11743775	1.00[ASN][1000 genomes]
rs11744033	0.91[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744325	1.00[ASN][1000 genomes]
rs11949884	0.95[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951675	0.91[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952993	1.00[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955946	1.00[CEU][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.89[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];0.81[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188094	1.00[ASN][1000 genomes]
rs12188249	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188655	1.00[ASN][1000 genomes]
rs12189005	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658697	0.81[YRI][hapmap]
rs13152882	0.87[YRI][hapmap]
rs17571029	0.91[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17572843	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]
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	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55792004	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55941525	1.00[ASN][1000 genomes]
rs56051320	1.00[ASN][1000 genomes]
rs56099704	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56106025	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56258383	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62374052	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376462	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376463	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376490	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62376491	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452927	0.91[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509877	1.00[ASN][1000 genomes]
rs6860216	1.00[ASN][1000 genomes]
rs6861614	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6880626	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886773	0.91[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888672	1.00[ASN][1000 genomes]
rs6888979	1.00[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889138	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[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	0.86[AMR][1000 genomes];0.84[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	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	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
4	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
rs10514343	GPR98	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90309800-90323200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90314800-90323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:90314800-90327000	Weak transcription	Gastric	stomach
4	chr5:90316600-90323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:90317000-90323200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:90317000-90325000	Enhancers	Colon Smooth Muscle	Colon
7	chr5:90317600-90324600	Enhancers	Stomach Mucosa	stomach
8	chr5:90317800-90323000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:90318400-90324200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:90318600-90323800	Weak transcription	K562	blood
11	chr5:90318800-90323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:90318800-90323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:90319400-90323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:90319400-90324600	Enhancers	Fetal Lung	lung
15	chr5:90319600-90323200	Weak transcription	Fetal Intestine Small	intestine
16	chr5:90319800-90324400	Enhancers	Fetal Stomach	stomach
17	chr5:90320200-90323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:90320800-90326800	Weak transcription	NHEK	skin
19	chr5:90321000-90324000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:90321400-90323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:90321600-90323000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:90321600-90324000	Enhancers	HepG2	liver
23	chr5:90321600-90325000	Enhancers	Liver	Liver
24	chr5:90321800-90323000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:90321800-90323200	Weak transcription	Adipose Nuclei	Adipose
26	chr5:90321800-90323200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:90322000-90323200	Weak transcription	Small Intestine	intestine
28	chr5:90322200-90324000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:90322200-90327400	Enhancers	A549	lung
30	chr5:90322400-90323200	Weak transcription	Fetal Intestine Large	intestine
31	chr5:90322400-90323200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:90322400-90324800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:90322600-90323000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:90322600-90325000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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