Variant report

Variant	rs56233242
Chromosome Location	chr7:50634053-50634054
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:50634035-50634085	ovcar-3	ovarian:	n/a
2	chr7:50634035-50634085	T-47D	breast:	n/a
3	chr7:50634035-50634085	PANC-1	pancreas:	n/a
4	chr7:50634035-50634085	H1-hESC	embryonic stem cell:	embryo
5	chr7:50634035-50634085	Hepatocyte	liver:	n/a
6	chr7:50634035-50634085	HNPCEpiC	eye:	n/a
7	chr7:50634035-50634085	K562	blood:	n/a
8	chr7:50634035-50634085	PFSK-1	brain:	n/a
9	chr7:50634035-50634085	GM12891	blood:	n/a
10	chr7:50634035-50634085	PrEC	prostate:	n/a
11	chr7:50634035-50634085	HepG2	liver:	n/a
12	chr7:50634035-50634085	Jurkat	blood:	n/a
13	chr7:50634035-50634085	AG10803	skin:	n/a
14	chr7:50634035-50634085	HL-60	blood:	n/a
15	chr7:50634035-50634085	GM19239	blood:	n/a
16	chr7:50634035-50634085	Hela-S3	cervix:	n/a
17	chr7:50634035-50634085	HAEpiC	amniotic membrane:	n/a
18	chr7:50634035-50634085	LNCaP	prostate:	n/a
19	chr7:50634035-50634085	HCPEpiC	choroid plexus:	n/a
20	chr7:50634035-50634085	NB4	blood:	n/a
21	chr7:50634035-50634085	IMR90	lung:	fetal
22	chr7:50634035-50634085	HEEpiC	esophagus:	n/a
23	chr7:50634035-50634085	NHDF-neo	bronchial:	n/a
24	chr7:50634035-50634085	ECC-1	luminal epithelium:	n/a
25	chr7:50634035-50634085	HMEC	breast:	n/a
26	chr7:50634035-50634085	HEK293	kidney:	embryo
27	chr7:50634035-50634085	NH-A	brain:	n/a
28	chr7:50634035-50634085	BE2_C	brain:	n/a
29	chr7:50634035-50634085	HCM	heart:	n/a
30	chr7:50634035-50634085	BJ	skin:	n/a
31	chr7:50634035-50634085	GM06990	blood:	n/a
32	chr7:50634035-50634085	CMK	blood:	n/a
33	chr7:50634035-50634085	NT2-D1	testis:	n/a
34	chr7:50634035-50634085	SKMC	muscle:	n/a
35	chr7:50634035-50634085	AG04450	lung:	fetal
36	chr7:50634035-50634085	HPAEpiC	pulmonary alveolar:	n/a
37	chr7:50634035-50634085	NHBE	bronchial:	n/a
38	chr7:50634035-50634085	Caco-2	colon:	n/a
39	chr7:50634035-50634085	U87	brain:	n/a
40	chr7:50634035-50634085	AoSMC	blood vessel:	n/a
41	chr7:50634035-50634085	HCT-116	colon:	n/a
42	chr7:50634035-50634085	AG09319	gingival:	n/a
43	chr7:50634035-50634085	MCF-7	breast:	n/a
44	chr7:50634035-50634085	SK-N-SH_RA	brain:	n/a
45	chr7:50634035-50634085	HRE	kidney:	n/a
46	chr7:50634035-50634085	SAEC	small airway:	n/a
47	chr7:50634035-50634085	RPTEC	kidney:	n/a
48	chr7:50634035-50634085	HUVEC	blood vessel:	n/a
49	chr7:50634035-50634085	SK-N-MC	brain:	n/a
50	chr7:50634035-50634085	AG09309	skin:	n/a

No data

Variant related genes	Relation type
DDC	CpG island

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10238413	0.82[ASN][1000 genomes]
rs10274172	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10278338	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238214	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11238226	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11489734	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11489736	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11977415	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665904	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12669770	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1813214	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1839740	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1966839	0.82[EUR][1000 genomes]
rs1987859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829897	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4275187	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4392851	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4452748	0.80[EUR][1000 genomes]
rs4469404	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4512339	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4601266	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947684	0.82[ASN][1000 genomes]
rs55718635	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738142	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59086818	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6593010	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68143668	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73125288	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73125290	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7797131	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7802148	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56233242	FIGNL1	cis	lung	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50620800-50635600	Weak transcription	Lung	lung
2	chr7:50633200-50634200	Enhancers	Liver	Liver
3	chr7:50633200-50634200	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr7:50633200-50634200	Enhancers	Pancreas	Pancrea
5	chr7:50633200-50634200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr7:50633600-50634200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr7:50633600-50635800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:50633800-50634400	Enhancers	HepG2	liver
9	chr7:50633800-50635200	Enhancers	Fetal Intestine Large	intestine
10	chr7:50633800-50635600	Enhancers	Fetal Intestine Small	intestine
11	chr7:50634000-50634200	Enhancers	Colonic Mucosa	Colon
12	chr7:50634000-50634200	Enhancers	Rectal Mucosa Donor 29	rectum

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