Variant report

Variant	rs58298367
Chromosome Location	chr7:50519682-50519683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50518383..50520516-chr7:50572098..50575046,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FIGNL1-1	chr7:50518506-50521012	ENSG00000248258
2	lnc-FIGNL1-1	chr7:50518449-50521151	XLOC_006441

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11575564	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1470746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133828	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17553002	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17553022	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17634434	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17634488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5014165	0.85[ASN][1000 genomes]
rs56819103	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57145809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57345445	0.84[EUR][1000 genomes]
rs58744984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59913779	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60056150	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61731356	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72645704	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72645705	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72645706	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72645707	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72645709	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779747	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779917	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7792486	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs58298367	IKZF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50518800-50521600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:50518800-50522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:50518800-50535400	Weak transcription	Pancreas	Pancrea
4	chr7:50518800-50535600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:50518800-50535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:50518800-50535600	Weak transcription	HepG2	liver
7	chr7:50519000-50523400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:50519000-50523400	Weak transcription	Liver	Liver
9	chr7:50519000-50523400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:50519000-50523800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:50519000-50523800	Weak transcription	Fetal Intestine Small	intestine
12	chr7:50519000-50524400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:50519000-50529400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:50519200-50523400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:50519200-50524000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:50519200-50524000	Weak transcription	Fetal Intestine Large	intestine
17	chr7:50519400-50522600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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