Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50486332..50488429-chr7:50495573..50497153,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10215297	0.84[EUR][1000 genomes]
rs10216316	0.82[EUR][1000 genomes]
rs10224094	0.92[ASN][1000 genomes]
rs10235371	1.00[YRI][hapmap];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	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11980407	1.00[JPT][hapmap]
rs2329343	1.00[YRI][hapmap]
rs28573146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265140	1.00[YRI][hapmap]
rs4947396	1.00[YRI][hapmap]
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]
rs6264	1.00[YRI][hapmap]
rs6944602	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944650	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6952409	0.84[EUR][1000 genomes]
rs6972091	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6972476	1.00[YRI][hapmap]
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
rs1002371	IKZF1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50483400-50488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:50484600-50489000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:50484600-50489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:50484800-50488400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:50484800-50488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:50485000-50490800	Weak transcription	Spleen	Spleen
7	chr7:50485400-50490400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:50486200-50513200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:50486400-50488800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:50486400-50491600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr7:50486600-50489000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:50486600-50495000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:50486800-50491400	Weak transcription	Fetal Thymus	thymus
14	chr7:50487000-50489000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:50488000-50489800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr7:50488200-50488600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:50488200-50489400	Enhancers	HUES6 Cell Line	embryonic stem cell

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