Variant report

Variant	rs991570
Chromosome Location	chr5:35805208-35805209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12153578	0.93[JPT][hapmap]
rs12521860	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs13436632	0.96[CEU][hapmap];0.81[JPT][hapmap];0.98[EUR][1000 genomes]
rs1494572	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961426	0.83[EUR][1000 genomes]
rs4869485	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4869672	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6451229	0.84[CEU][hapmap]
rs6451234	0.87[JPT][hapmap]
rs716302	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7736291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903388	0.92[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs903389	0.92[CEU][hapmap];0.89[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs991570	IL7R	cis	parietal	SCAN
rs991570	PDZD2	cis	cerebellum	SCAN
rs991570	PDZD2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35801800-35807800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:35802200-35807800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr5:35802200-35808400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:35802400-35805800	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr5:35802400-35807800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:35802600-35805400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:35802600-35805600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:35802800-35805600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:35803000-35805800	Enhancers	Brain Germinal Matrix	brain
10	chr5:35803400-35809400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:35803400-35809400	Weak transcription	Fetal Kidney	kidney
12	chr5:35803600-35805400	Enhancers	Brain Hippocampus Middle	brain
13	chr5:35803600-35805400	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr5:35803600-35805600	Enhancers	Primary T cells from cord blood	blood
15	chr5:35803800-35805800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:35803800-35810600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:35803800-35813800	Weak transcription	Left Ventricle	heart
18	chr5:35804400-35809800	Weak transcription	Spleen	Spleen
19	chr5:35804600-35806400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:35804600-35809800	Weak transcription	Thymus	Thymus
21	chr5:35804800-35807400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr5:35804800-35807400	Weak transcription	Fetal Thymus	thymus
23	chr5:35804800-35807800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:35804800-35809800	Weak transcription	Dnd41	blood
25	chr5:35805000-35807200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr5:35805200-35806400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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