Variant report

Variant	rs6745099
Chromosome Location	chr2:100739441-100739442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10177007	0.94[EUR][1000 genomes]
rs10199628	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211423	0.89[CEU][hapmap]
rs13392222	0.83[EUR][1000 genomes]
rs17023453	0.84[EUR][1000 genomes]
rs17023459	0.84[EUR][1000 genomes]
rs17023512	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023516	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17023563	1.00[ASN][1000 genomes]
rs17023571	1.00[ASN][1000 genomes]
rs17023655	1.00[ASN][1000 genomes]
rs17352745	0.82[EUR][1000 genomes]
rs17352801	0.82[EUR][1000 genomes]
rs17352808	0.82[EUR][1000 genomes]
rs17437282	0.82[EUR][1000 genomes]
rs17437338	0.82[EUR][1000 genomes]
rs2309776	0.89[EUR][1000 genomes]
rs56993260	1.00[ASN][1000 genomes]
rs62148113	1.00[ASN][1000 genomes]
rs62148114	1.00[ASN][1000 genomes]
rs62148119	1.00[ASN][1000 genomes]
rs62149319	0.80[EUR][1000 genomes]
rs62149320	0.82[EUR][1000 genomes]
rs62149321	0.82[EUR][1000 genomes]
rs62149341	0.82[EUR][1000 genomes]
rs62149343	0.86[EUR][1000 genomes]
rs62149354	1.00[ASN][1000 genomes]
rs62150260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150261	1.00[ASN][1000 genomes]
rs62150270	1.00[ASN][1000 genomes]
rs62150271	1.00[ASN][1000 genomes]
rs62150274	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62150289	1.00[ASN][1000 genomes]
rs6743817	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748652	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750214	0.81[EUR][1000 genomes]
rs72819167	0.82[EUR][1000 genomes]
rs72819176	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72819177	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72819179	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72819180	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72819181	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7601715	1.00[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	nsv458707	chr2:100687778-100753490	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv582529	chr2:100687778-100753490	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6745099	ARID5A	cis	cerebellum	SCAN
rs6745099	ITPRIPL1	cis	parietal	SCAN
rs6745099	MFSD9	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100730200-100742200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:100730800-100746400	Weak transcription	Spleen	Spleen
3	chr2:100731800-100742000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:100732000-100749400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:100732000-100754400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:100734400-100748000	Weak transcription	Adipose Nuclei	Adipose
7	chr2:100734600-100742200	Weak transcription	Pancreas	Pancrea
8	chr2:100735000-100741000	Strong transcription	Dnd41	blood
9	chr2:100735800-100744200	Strong transcription	Primary hematopoietic stem cells	blood
10	chr2:100736600-100742400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:100736800-100740000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:100736800-100747400	Strong transcription	Primary B cells from cord blood	blood
13	chr2:100737400-100742200	Weak transcription	Thymus	Thymus
14	chr2:100737600-100739600	Weak transcription	Primary T cells from cord blood	blood
15	chr2:100738200-100741600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:100738200-100742400	Weak transcription	Fetal Thymus	thymus
17	chr2:100738400-100739600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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