Variant report

Variant	rs3807552
Chromosome Location	chr7:50610742-50610743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50605928..50607774-chr7:50609469..50611799,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IKZF1-1	chr7:50609943-50611161	ENSG00000226122.1

Variant related genes	Relation type
ENSG00000132437	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10239830	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249420	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[ASN][1000 genomes]
rs10265930	0.88[ASN][1000 genomes]
rs10267323	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10271341	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10276473	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277662	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11575320	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772714	0.81[CHB][hapmap]
rs12671474	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470747	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs17733244	0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2044859	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2329371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876829	0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs28889020	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3735273	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3735275	0.85[CHB][hapmap]
rs3779074	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3779078	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807556	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807558	0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs6950777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6963996	0.80[EUR][1000 genomes]
rs745042	0.84[JPT][hapmap]
rs745043	0.81[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap]
rs7776816	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779110	0.91[ASN][1000 genomes]
rs7786398	0.90[JPT][hapmap]
rs7790758	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7803440	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs7803788	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[ASN][1000 genomes]
rs7803903	0.91[ASN][1000 genomes]
rs896309	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs978784	0.85[GIH][hapmap]
rs9942686	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv429750	chr7:50603534-50622712	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv429752	chr7:50607353-50620030	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv429751	chr7:50607353-50622712	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3807552	FIGNL1	cis	parietal	SCAN
rs3807552	IKZF1	cis	lymphoblastoid	seeQTL
rs3807552	FIGNL1	cis	Thyroid	GTEx
rs3807552	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs3807552	FIGNL1	cis	Stomach	GTEx
rs3807552	FIGNL1	cis	lung	GTEx
rs3807552	FIGNL1	cis	cerebellum	SCAN
rs3807552	FIGNL1	cis	lymphoblastoid	seeQTL
rs3807552	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs3807552	FIGNL1	cis	Heart Left Ventricle	GTEx
rs3807552	FIGNL1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50600200-50612600	Weak transcription	Small Intestine	intestine
2	chr7:50600600-50619400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:50602600-50618200	Weak transcription	Pancreas	Pancrea
5	chr7:50602800-50613800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:50603600-50613000	Strong transcription	Duodenum Mucosa	Duodenum
7	chr7:50604000-50612000	Strong transcription	Fetal Intestine Large	intestine
8	chr7:50604400-50612000	Strong transcription	HepG2	liver
9	chr7:50604600-50612400	Strong transcription	Fetal Intestine Small	intestine
10	chr7:50607000-50612000	Weak transcription	Fetal Stomach	stomach
11	chr7:50609000-50611800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr7:50609600-50611600	Strong transcription	Liver	Liver
13	chr7:50610000-50611200	Weak transcription	Stomach Mucosa	stomach
14	chr7:50610200-50611000	Strong transcription	Colonic Mucosa	Colon
15	chr7:50610200-50611000	Enhancers	Placenta	Placenta
16	chr7:50610600-50611000	Weak transcription	Spleen	Spleen

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