Variant report

Variant	rs11980407
Chromosome Location	chr7:50471613-50471614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10230978	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10235371	1.00[JPT][hapmap]
rs10264390	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272724	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10278451	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1110701	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11552047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11575544	1.00[JPT][hapmap]
rs11575575	1.00[JPT][hapmap]
rs11978267	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11980379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133805	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17133807	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28462675	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696237	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58923657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62445866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62445869	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62447205	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62447208	0.83[AMR][1000 genomes]
rs6944650	1.00[JPT][hapmap]
rs6956014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960400	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6964969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973210	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11980407	IKZF1	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50431400-50472600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:50461600-50472600	Strong transcription	Dnd41	blood
3	chr7:50464400-50474400	Strong transcription	Thymus	Thymus
4	chr7:50464600-50472200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:50464800-50472200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:50464800-50472400	Strong transcription	Primary hematopoietic stem cells	blood
7	chr7:50464800-50472400	Strong transcription	Fetal Thymus	thymus
8	chr7:50465400-50472800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:50465600-50472600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:50465600-50473400	Strong transcription	Primary T cells from cord blood	blood
11	chr7:50465800-50472200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:50466400-50474600	Weak transcription	K562	blood
13	chr7:50466600-50473600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:50467000-50477200	Weak transcription	Colonic Mucosa	Colon
15	chr7:50467600-50472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:50468000-50472200	Strong transcription	GM12878-XiMat	blood
17	chr7:50468200-50479800	Weak transcription	Gastric	stomach
18	chr7:50469000-50472400	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr7:50469000-50476800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:50469000-50480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:50469800-50472600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:50470200-50472400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:50470200-50472800	Weak transcription	Spleen	Spleen
24	chr7:50470600-50472400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:50470600-50472400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:50470600-50485600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:50470800-50472400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr7:50470800-50477400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:50471000-50472200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:50471000-50472800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:50471200-50472200	Genic enhancers	Primary monocytes fromperipheralblood	blood
32	chr7:50471200-50474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:50471400-50472600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:50471400-50474400	Genic enhancers	Primary B cells from cord blood	blood
35	chr7:50471400-50474600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr7:50471600-50472600	Genic enhancers	Monocytes-CD14+_RO01746	blood

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