Variant report

Variant	rs7792486
Chromosome Location	chr7:50486309-50486310
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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 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	chr7:50484194..50487347-chr7:50489470..50493667,5	K562	blood:
4	chr7:50158832..50160033-chr7:50485413..50486368,7	MCF-7	breast:
5	chr7:50159434..50160127-chr7:50485653..50486534,3	K562	blood:
6	chr7:50181654..50182562-chr7:50485410..50486472,6	MCF-7	breast:
7	chr7:50473414..50475429-chr7:50484863..50486654,2	K562	blood:
8	chr7:50198460..50199386-chr7:50485402..50486365,4	K562	blood:
9	chr7:50485524..50486325-chr7:50496721..50497605,2	MCF-7	breast:
10	chr7:50131789..50132494-chr7:50485491..50486334,3	MCF-7	breast:
11	chr7:50244573..50245590-chr7:50485442..50486430,7	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FIGNL1-3	chr7:50485943-50488423	l_3413_chr7:50485640-50488510_testes

No data

Variant related genes	Relation type
ENSG00000228005	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11575564	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1470746	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17133828	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17133842	0.81[GIH][hapmap]
rs17553002	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17553022	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17634434	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17634488	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5014165	0.82[ASN][1000 genomes]
rs56819103	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57145809	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57345445	0.86[EUR][1000 genomes]
rs58298367	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58744984	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59913779	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60056150	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61731356	0.86[EUR][1000 genomes]
rs72645704	0.92[EUR][1000 genomes]
rs72645705	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72645706	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72645707	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72645709	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779747	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779917	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7792486	IKZF1	cis	Lymphoblastoid	GTEx
rs7792486	IKZF1	Cis_1M	lymphoblastoid	RTeQTL
rs7792486	ZNFN1A1	cis	multi-tissue	Pritchard
rs7792486	IKZF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50472400-50486400	Enhancers	Primary B cells from peripheral blood	blood
2	chr7:50483000-50486400	Enhancers	Thymus	Thymus
3	chr7:50483000-50486800	Enhancers	Fetal Thymus	thymus
4	chr7:50483400-50488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr7:50484600-50489000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:50484600-50489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:50484800-50488400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:50484800-50488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:50485000-50486400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:50485000-50490800	Weak transcription	Spleen	Spleen
11	chr7:50485400-50490400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:50485600-50486400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr7:50486000-50486400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:50486000-50486600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr7:50486000-50486800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr7:50486000-50486800	Enhancers	Fetal Intestine Small	intestine
17	chr7:50486000-50486800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr7:50486000-50486800	Enhancers	K562	blood
19	chr7:50486000-50487000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:50486200-50487000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:50486200-50487000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:50486200-50513200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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