Variant report

Variant	rs61742382
Chromosome Location	chr7:50518546-50518547
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr7:50517927-50518689	GM12878	blood:	n/a	chr7:50518150-50518166
2	POLR2A	chr7:50517607-50519010	SK-N-MC	brain:	n/a	n/a
3	CCNT2	chr7:50517530-50518678	K562	blood:	n/a	chr7:50517933-50517942 chr7:50517681-50517690
4	ELF1	chr7:50517491-50518638	GM12878	blood:	n/a	chr7:50518160-50518172
5	CTCF	chr7:50518460-50518610	GM12864	blood:	n/a	n/a
6	POLR2A	chr7:50517619-50518756	GM18951	blood:	n/a	n/a
7	POLR2A	chr7:50517783-50518701	GM10847	blood:	n/a	n/a
8	ZEB1	chr7:50517702-50518723	GM12878	blood:	n/a	chr7:50518150-50518161
9	POLR2A	chr7:50517648-50518659	Raji	blood:	n/a	n/a
10	PML	chr7:50517707-50518549	GM12878	blood:	n/a	n/a
11	MYC	chr7:50517855-50518737	MCF-7	breast:	n/a	chr7:50518140-50518149
12	RUNX3	chr7:50517469-50518770	GM12878	blood:	n/a	n/a
13	MYC	chr7:50517718-50518740	MCF-7	breast:	n/a	chr7:50518140-50518149
14	POLR2A	chr7:50517712-50518786	MCF-7	breast:	n/a	n/a
15	POLR2A	chr7:50517738-50518612	HL-60	blood:	n/a	n/a
16	CTCF	chr7:50518336-50518656	MCF-7	breast:	n/a	n/a
17	E2F6	chr7:50517557-50518844	H1-hESC	embryonic stem cell:	n/a	chr7:50517681-50517690 chr7:50517973-50517982 chr7:50518051-50518060
18	MAX	chr7:50517524-50518922	A549	lung:	n/a	chr7:50518140-50518149
19	POLR2A	chr7:50517723-50518789	GM15510	blood:	n/a	n/a
20	ZNF263	chr7:50517463-50518620	HEK293-T-REx	kidney:	n/a	n/a
21	POLR2A	chr7:50517750-50518692	A549	lung:	n/a	n/a
22	POLR2A	chr7:50517643-50518729	MCF-7	breast:	n/a	n/a
23	POLR2A	chr7:50518294-50518674	A549	lung:	n/a	n/a
24	MYC	chr7:50518519-50518693	MCF-7	breast:	n/a	n/a
25	POLR2A	chr7:50517547-50518779	GM19099	blood:	n/a	n/a
26	POLR2A	chr7:50517688-50518734	HL-60	blood:	n/a	n/a
27	CTCF	chr7:50518480-50518630	GM12867	blood:	n/a	n/a
28	HCFC1	chr7:50517589-50518589	K562	blood:	n/a	n/a
29	POLR2A	chr7:50517710-50518724	A549	lung:	n/a	n/a
30	POLR2A	chr7:50517542-50518786	GM12892	blood:	n/a	n/a
31	POLR2A	chr7:50517811-50518881	GM12891	blood:	n/a	n/a
32	MAX	chr7:50517623-50518899	MCF-7	breast:	n/a	chr7:50518140-50518149
33	RCOR1	chr7:50517810-50518627	GM12878	blood:	n/a	n/a
34	MAX	chr7:50517535-50518860	MCF-7	breast:	n/a	chr7:50518140-50518149
35	CTCF	chr7:50518500-50518650	GM12866	blood:	n/a	n/a
36	POLR2A	chr7:50517779-50518826	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:50517659-50518682	GM19193	blood:	n/a	n/a
38	YY1	chr7:50517987-50518613	GM12892	blood:	n/a	n/a
39	HMGN3	chr7:50517538-50518668	K562	blood:	n/a	n/a
40	E2F6	chr7:50517676-50518643	A549	lung:	n/a	chr7:50517681-50517690 chr7:50517973-50517982 chr7:50518051-50518060
41	CTCF	chr7:50518480-50518630	GM12870	blood:	n/a	n/a
42	POLR2A	chr7:50517641-50518780	GM18526	blood:	n/a	n/a
43	CTCF	chr7:50518364-50518666	MCF-7	breast:	n/a	n/a
44	MAX	chr7:50517618-50518870	H1-hESC	embryonic stem cell:	n/a	chr7:50518140-50518149
45	E2F6	chr7:50517635-50518786	H1-hESC	embryonic stem cell:	n/a	chr7:50517681-50517690 chr7:50517973-50517982 chr7:50518051-50518060
46	POLR2A	chr7:50517825-50518737	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr7:50517677-50518796	GM18505	blood:	n/a	n/a
48	E2F6	chr7:50517578-50518621	K562	blood:	n/a	chr7:50517681-50517690 chr7:50517973-50517982 chr7:50518051-50518060
49	POLR2A	chr7:50517703-50518548	ProgFib	skin:	n/a	n/a
50	E2F6	chr7:50517500-50518903	A549	lung:	n/a	chr7:50517681-50517690 chr7:50517973-50517982 chr7:50518051-50518060

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

Variant related genes	Relation type
FIGNL1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11575551	1.00[AMR][1000 genomes]
rs11575552	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11575557	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11575565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11575568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11575570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11575574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11971146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11971434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11973116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11973441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11974930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11975450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11976368	0.90[AFR][1000 genomes]
rs11977135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11978010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17133817	0.88[AFR][1000 genomes]
rs17133826	0.88[AFR][1000 genomes]
rs17133832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17152012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36117815	1.00[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50516800-50518800	Active TSS	NHLF	lung
2	chr7:50516800-50519000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:50517000-50518600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr7:50517000-50518800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:50517000-50518800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:50517000-50518800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:50517200-50518600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr7:50517200-50518600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:50517200-50518600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:50517200-50518600	Active TSS	Gastric	stomach
11	chr7:50517200-50518600	Active TSS	Hela-S3	cervix
12	chr7:50517200-50518600	Flanking Active TSS	HMEC	breast
13	chr7:50517200-50518800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr7:50517200-50518800	Flanking Active TSS	Liver	Liver
15	chr7:50517200-50518800	Active TSS	Ovary	ovary
16	chr7:50517400-50518600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr7:50517400-50518600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:50517400-50518600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:50517400-50518600	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr7:50517400-50518600	Active TSS	Aorta	Aorta
21	chr7:50517400-50518600	Active TSS	Brain Cingulate Gyrus	brain
22	chr7:50517400-50518600	Active TSS	Brain Hippocampus Middle	brain
23	chr7:50517400-50518600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:50517400-50518600	Active TSS	Duodenum Mucosa	Duodenum
25	chr7:50517400-50518600	Active TSS	Fetal Lung	lung
26	chr7:50517400-50518600	Active TSS	Right Atrium	heart
27	chr7:50517400-50518600	Active TSS	Thymus	Thymus
28	chr7:50517400-50518600	Active TSS	HSMM	muscle
29	chr7:50517400-50518600	Active TSS	NHDF-Ad	bronchial
30	chr7:50517400-50518800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr7:50517400-50518800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:50517400-50518800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr7:50517400-50518800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:50517400-50518800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:50517400-50518800	Active TSS	Colonic Mucosa	Colon
36	chr7:50517400-50518800	Active TSS	Fetal Kidney	kidney
37	chr7:50517400-50518800	Active TSS	Left Ventricle	heart
38	chr7:50517400-50518800	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr7:50517400-50519000	Active TSS	Colon Smooth Muscle	Colon
40	chr7:50517400-50519000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr7:50517400-50519000	Active TSS	A549	lung
42	chr7:50517600-50518600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:50517600-50518600	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr7:50517600-50518600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr7:50517600-50518600	Active TSS	Primary T cells from cord blood	blood
46	chr7:50517600-50518600	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr7:50517600-50518600	Active TSS	Brain Substantia Nigra	brain
48	chr7:50517600-50518600	Active TSS	Fetal Intestine Small	intestine
49	chr7:50517600-50518600	Active TSS	Small Intestine	intestine
50	chr7:50517600-50518800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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