Variant report

Variant	rs17553022
Chromosome Location	chr7:50483454-50483455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11575564	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1470746	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17133828	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17133842	0.90[YRI][hapmap]
rs17553002	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17634434	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17634488	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5014165	0.82[ASN][1000 genomes]
rs56819103	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57145809	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57345445	0.86[EUR][1000 genomes]
rs58298367	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58744984	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59913779	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60056150	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61731356	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72645704	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs72645705	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72645706	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72645707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72645709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779747	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7792486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv515738	chr7:50476109-50494207	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17553022	IKZF1	cis	Lymphoblastoid	GTEx
rs17553022	IKZF1	Cis_1M	lymphoblastoid	RTeQTL
rs17553022	ZNFN1A1	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50470600-50485600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:50472200-50483800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:50472400-50486400	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:50474400-50483600	Enhancers	Primary B cells from cord blood	blood
5	chr7:50475400-50483800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:50478600-50483600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:50478800-50483800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:50479200-50483600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:50479400-50483600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:50479600-50483600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:50481000-50483600	Weak transcription	Adipose Nuclei	Adipose
12	chr7:50481400-50486000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:50481600-50486200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:50482800-50483800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr7:50482800-50485600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr7:50483000-50485600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr7:50483000-50486400	Enhancers	Thymus	Thymus
18	chr7:50483000-50486800	Enhancers	Fetal Thymus	thymus
19	chr7:50483200-50483600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr7:50483200-50484000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr7:50483200-50484000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:50483200-50484200	Enhancers	Placenta	Placenta
23	chr7:50483200-50484200	Enhancers	GM12878-XiMat	blood
24	chr7:50483200-50484400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:50483200-50485400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:50483200-50486200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:50483400-50485000	Enhancers	Spleen	Spleen
28	chr7:50483400-50485200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr7:50483400-50485600	Enhancers	Primary T cells from cord blood	blood
30	chr7:50483400-50485600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr7:50483400-50486200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr7:50483400-50486200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr7:50483400-50488800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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