Variant report

Variant	rs6882117
Chromosome Location	chr5:35808747-35808748
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11948206	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12521860	0.86[JPT][hapmap]
rs13164644	0.81[EUR][1000 genomes]
rs13436632	0.86[JPT][hapmap]
rs1389836	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[EUR][1000 genomes]
rs1389837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36093359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4869672	0.92[JPT][hapmap]
rs57186765	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903389	0.92[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6882117	IL7R	cis	parietal	SCAN
rs6882117	PDZD2	cis	cerebellum	SCAN
rs6882117	NIPBL	cis	parietal	SCAN
rs6882117	WDR70	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35803400-35809400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:35803400-35809400	Weak transcription	Fetal Kidney	kidney
3	chr5:35803800-35810600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr5:35803800-35813800	Weak transcription	Left Ventricle	heart
5	chr5:35804400-35809800	Weak transcription	Spleen	Spleen
6	chr5:35804600-35809800	Weak transcription	Thymus	Thymus
7	chr5:35804800-35809800	Weak transcription	Dnd41	blood
8	chr5:35806600-35816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:35807600-35809800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:35808000-35809200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:35808000-35810400	Weak transcription	Fetal Thymus	thymus
12	chr5:35808200-35808800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:35808200-35809200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:35808200-35809200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:35808200-35809400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr5:35808200-35810600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:35808400-35808800	Weak transcription	Primary T cells from cord blood	blood
18	chr5:35808400-35808800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:35808400-35808800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:35808400-35808800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:35808400-35808800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:35808400-35808800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:35808400-35808800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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