Variant report

Variant	rs28573146
Chromosome Location	chr7:50485589-50485590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:50181242..50182508-chr7:50485453..50486419,3	K562	blood:
2	chr7:50484672..50487398-chr7:50490393..50493667,4	K562	blood:
3	chr7:50244665..50245593-chr7:50485405..50486013,4	MCF-7	breast:
4	chr7:50484194..50487347-chr7:50489470..50493667,5	K562	blood:
5	chr7:50158832..50160033-chr7:50485413..50486368,7	MCF-7	breast:
6	chr7:50247609..50248195-chr7:50485491..50486034,2	K562	blood:
7	chr7:50181654..50182562-chr7:50485410..50486472,6	MCF-7	breast:
8	chr7:50188357..50189315-chr7:50485544..50486298,2	K562	blood:
9	chr7:50473414..50475429-chr7:50484863..50486654,2	K562	blood:
10	chr7:50198460..50199386-chr7:50485402..50486365,4	K562	blood:
11	chr7:50485524..50486325-chr7:50496721..50497605,2	MCF-7	breast:
12	chr7:50131789..50132494-chr7:50485491..50486334,3	MCF-7	breast:
13	chr7:50313145..50313783-chr7:50485463..50486082,2	MCF-7	breast:
14	chr7:50244500..50246080-chr7:50485390..50486198,6	K562	blood:
15	chr7:50131802..50132527-chr7:50485456..50486116,2	K562	blood:
16	chr7:50244573..50245590-chr7:50485442..50486430,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228005	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1002371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215297	0.84[EUR][1000 genomes]
rs10216316	0.82[EUR][1000 genomes]
rs10224094	0.92[ASN][1000 genomes]
rs10235371	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10236132	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10250794	0.88[ASN][1000 genomes]
rs10261922	0.85[ASN][1000 genomes]
rs10270682	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10273657	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11575544	0.81[ASN][1000 genomes]
rs11575575	0.88[ASN][1000 genomes]
rs55693922	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs55981617	0.84[EUR][1000 genomes]
rs56156635	0.84[EUR][1000 genomes]
rs61731355	0.83[EUR][1000 genomes]
rs62447207	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62447208	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944602	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944650	0.88[ASN][1000 genomes]
rs6952409	0.84[EUR][1000 genomes]
rs6972091	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9656639	0.91[AFR][1000 genomes];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28573146	IKZF1	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 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	chr7:50472400-50486400	Enhancers	Primary B cells from peripheral blood	blood
3	chr7:50481400-50486000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:50481600-50486200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:50482800-50485600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr7:50483000-50485600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr7:50483000-50486400	Enhancers	Thymus	Thymus
8	chr7:50483000-50486800	Enhancers	Fetal Thymus	thymus
9	chr7:50483200-50486200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:50483400-50485600	Enhancers	Primary T cells from cord blood	blood
11	chr7:50483400-50485600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr7:50483400-50486200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:50483400-50486200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:50483400-50488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:50483600-50485600	Enhancers	Primary hematopoietic stem cells	blood
16	chr7:50483600-50485600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr7:50484600-50486000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:50484600-50486000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:50484600-50486000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr7:50484600-50486200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr7:50484600-50489000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:50484600-50489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:50484800-50485600	Enhancers	GM12878-XiMat	blood
24	chr7:50484800-50486000	Weak transcription	K562	blood
25	chr7:50484800-50486200	Enhancers	Primary B cells from cord blood	blood
26	chr7:50484800-50488400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:50484800-50488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:50485000-50485600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:50485000-50486200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:50485000-50486400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr7:50485000-50490800	Weak transcription	Spleen	Spleen
32	chr7:50485200-50486200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr7:50485400-50485600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr7:50485400-50490400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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