Variant report

Variant	rs2060762
Chromosome Location	chr7:50529384-50529385
allele	A/G
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:3)
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	chr7:50529359-50529409	K562	blood:	n/a
2	chr7:50529359-50529409	U87	brain:	n/a
3	chr7:50529359-50529409	HCF	heart:	n/a
4	chr7:50529359-50529409	H1-hESC	embryonic stem cell:	embryo
5	chr7:50529359-50529409	ProgFib	skin:	n/a
6	chr7:50529359-50529409	SK-N-SH	brain:	n/a
7	chr7:50529359-50529409	HCT-116	colon:	n/a
8	chr7:50529359-50529409	HRCEpiC	kidney:	n/a
9	chr7:50529359-50529409	GM12878	blood:	n/a
10	chr7:50529359-50529409	HMEC	breast:	n/a
11	chr7:50529359-50529409	Jurkat	blood:	n/a
12	chr7:50529359-50529409	HEK293	kidney:	embryo
13	chr7:50529359-50529409	HRE	kidney:	n/a
14	chr7:50529359-50529409	HL-60	blood:	n/a
15	chr7:50529359-50529409	IMR90	lung:	fetal
16	chr7:50529359-50529409	HRPEpiC	eye:	n/a
17	chr7:50529359-50529409	BE2_C	brain:	n/a
18	chr7:50529359-50529409	AG09309	skin:	n/a
19	chr7:50529359-50529409	PrEC	prostate:	n/a
20	chr7:50529359-50529409	NH-A	brain:	n/a
21	chr7:50529359-50529409	PANC-1	pancreas:	n/a
22	chr7:50529359-50529409	MCF10A-Er-Src	breast:	n/a
23	chr7:50529359-50529409	Hela-S3	cervix:	n/a
24	chr7:50529359-50529409	ECC-1	luminal epithelium:	n/a
25	chr7:50529359-50529409	AG09319	gingival:	n/a
26	chr7:50529359-50529409	Hepatocyte	liver:	n/a
27	chr7:50529359-50529409	GM19239	blood:	n/a
28	chr7:50529359-50529409	HAEpiC	amniotic membrane:	n/a
29	chr7:50529359-50529409	SKMC	muscle:	n/a
30	chr7:50529359-50529409	PFSK-1	brain:	n/a
31	chr7:50529359-50529409	NT2-D1	testis:	n/a
32	chr7:50529359-50529409	T-47D	breast:	n/a
33	chr7:50529359-50529409	HUVEC	blood vessel:	n/a
34	chr7:50529359-50529409	HCM	heart:	n/a
35	chr7:50529359-50529409	HEEpiC	esophagus:	n/a
36	chr7:50529359-50529409	NHBE	bronchial:	n/a
37	chr7:50529359-50529409	NHDF-neo	bronchial:	n/a
38	chr7:50529359-50529409	CMK	blood:	n/a
39	chr7:50529359-50529409	GM12891	blood:	n/a
40	chr7:50529359-50529409	SAEC	small airway:	n/a
41	chr7:50529359-50529409	AoSMC	blood vessel:	n/a
42	chr7:50529359-50529409	AG10803	skin:	n/a
43	chr7:50529359-50529409	ovcar-3	ovarian:	n/a
44	chr7:50529359-50529409	BJ	skin:	n/a
45	chr7:50529359-50529409	AG04450	lung:	fetal
46	chr7:50529359-50529409	GM06990	blood:	n/a
47	chr7:50529359-50529409	GM12892	blood:	n/a
48	chr7:50529359-50529409	HPAEpiC	pulmonary alveolar:	n/a
49	chr7:50529359-50529409	HNPCEpiC	eye:	n/a
50	chr7:50529359-50529409	LNCaP	prostate:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:50525809..50527390-chr7:50527778..50530476,2	K562	blood:
2	chr7:50517207..50520150-chr7:50528801..50531186,2	MCF-7	breast:
3	chr7:50527491..50529507-chr7:50534060..50535878,2	K562	blood:

No data

Variant related genes	Relation type
DDC	CpG island
ENSG00000132436	Chromatin interaction
ENSG00000132437	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10230343	0.95[JPT][hapmap]
rs11238134	0.86[YRI][hapmap]
rs11575463	0.85[YRI][hapmap]
rs11761683	0.87[YRI][hapmap]
rs11772714	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs1466164	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1807066	0.81[ASN][1000 genomes]
rs2060761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242042	0.90[AFR][1000 genomes]
rs2305358	0.86[JPT][hapmap]
rs2876829	0.83[YRI][hapmap]
rs3735273	0.84[CHB][hapmap]
rs3735275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807558	0.83[YRI][hapmap]
rs4515495	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947410	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947437	0.99[ASN][1000 genomes]
rs4947510	0.95[JPT][hapmap]
rs6593336	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945253	0.82[JPT][hapmap]
rs6965721	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745043	0.81[CHB][hapmap];0.84[CHD][hapmap];0.82[YRI][hapmap]
rs7790230	0.95[JPT][hapmap]
rs7790758	0.91[YRI][hapmap]
rs896309	0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs963739	0.90[EUR][1000 genomes];0.99[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	nsv1026081	chr7:50525900-50538184	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2060762	FIGNL1	cis	parietal	SCAN
rs2060762	FIGNL1	cis	multi-tissue	Pritchard
rs2060762	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs2060762	FIGNL1	cis	cerebellum	SCAN
rs2060762	FIGNL1	cis	Artery Tibial	GTEx
rs2060762	FIGNL1	cis	lung	GTEx
rs2060762	FIGNL1	cis	Nerve Tibial	GTEx
rs2060762	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2060762	FIGNL1	cis	lymphoblastoid	seeQTL
rs2060762	FIGNL1	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50518800-50535400	Weak transcription	Pancreas	Pancrea
2	chr7:50518800-50535600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:50518800-50535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:50518800-50535600	Weak transcription	HepG2	liver
5	chr7:50519000-50529400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:50524800-50530000	Weak transcription	Liver	Liver
7	chr7:50528800-50533800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr7:50528800-50535400	Weak transcription	Colonic Mucosa	Colon
9	chr7:50529200-50529600	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr7:50529200-50535600	Strong transcription	Fetal Intestine Large	intestine

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