Variant report

Variant	rs7558817
Chromosome Location	chr2:100654482-100654483
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10209110	0.93[ASN][1000 genomes]
rs10211595	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs10496344	0.81[CEU][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs1062143	0.97[ASN][1000 genomes]
rs11123804	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123805	0.98[ASN][1000 genomes]
rs11123810	0.81[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11123812	0.81[CEU][hapmap]
rs1115910	0.99[ASN][1000 genomes]
rs11681737	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11681966	0.81[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11685341	0.82[ASN][1000 genomes]
rs11690905	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs12712062	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712063	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12995420	0.99[ASN][1000 genomes]
rs12997584	0.99[ASN][1000 genomes]
rs13003982	0.85[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs13415583	0.81[CEU][hapmap]
rs1370356	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1821828	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1821829	0.84[ASN][1000 genomes]
rs2309748	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2576678	0.93[ASN][1000 genomes]
rs2871326	0.97[ASN][1000 genomes]
rs4850921	0.81[CEU][hapmap]
rs6542905	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714788	0.91[ASN][1000 genomes]
rs6733895	0.96[ASN][1000 genomes]
rs6750720	0.88[ASN][1000 genomes]
rs6754099	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582731	0.91[ASN][1000 genomes]
rs7599083	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7605430	0.99[ASN][1000 genomes]
rs9308833	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs961788	0.99[ASN][1000 genomes]

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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS 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	4 gene(s)	inside rSNPs	diseases
3	esv3425414	chr2:100652945-100655493	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv3361725	chr2:100653170-100655468	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7558817	MRPL30	cis	cerebellum	SCAN
rs7558817	FER1L5	cis	parietal	SCAN
rs7558817	AFF3	cis	parietal	SCAN
rs7558817	MGAT4A	cis	parietal	SCAN
rs7558817	COX5B	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100624800-100657800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:100633600-100660600	Weak transcription	Lung	lung
3	chr2:100637200-100658400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:100639000-100660600	Weak transcription	Primary T cells from cord blood	blood
5	chr2:100639600-100657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:100644600-100668400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:100646400-100662600	Weak transcription	Gastric	stomach
8	chr2:100648200-100666800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:100650600-100656800	Weak transcription	Fetal Brain Female	brain
10	chr2:100651800-100659600	Weak transcription	Left Ventricle	heart
11	chr2:100652000-100656200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:100652800-100661400	Weak transcription	Ovary	ovary
13	chr2:100653000-100656000	Weak transcription	Primary B cells from cord blood	blood
14	chr2:100653200-100667200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:100653600-100654600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:100653600-100656800	Weak transcription	Fetal Heart	heart
17	chr2:100653600-100657600	Weak transcription	Fetal Lung	lung
18	chr2:100653800-100657800	Weak transcription	Fetal Brain Male	brain
19	chr2:100654200-100654600	Weak transcription	Thymus	Thymus

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