Variant report

Variant	rs7520777
Chromosome Location	chr1:171216717-171216718
allele	C/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:2)
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	chr1:171216672-171216722	HCF	heart:	n/a
2	chr1:171216672-171216722	Caco-2	colon:	n/a
3	chr1:171216672-171216722	CMK	blood:	n/a
4	chr1:171216672-171216722	HRCEpiC	kidney:	n/a
5	chr1:171216672-171216722	PrEC	prostate:	n/a
6	chr1:171216672-171216722	H1-hESC	embryonic stem cell:	embryo
7	chr1:171216672-171216722	IMR90	lung:	fetal
8	chr1:171216672-171216722	HL-60	blood:	n/a
9	chr1:171216672-171216722	AG04449	skin:	fetal
10	chr1:171216672-171216722	AG09309	skin:	n/a
11	chr1:171216672-171216722	HEEpiC	esophagus:	n/a
12	chr1:171216672-171216722	HIPEpiC	eye:	n/a
13	chr1:171216672-171216722	HRE	kidney:	n/a
14	chr1:171216672-171216722	GM19239	blood:	n/a
15	chr1:171216672-171216722	Jurkat	blood:	n/a
16	chr1:171216672-171216722	PANC-1	pancreas:	n/a
17	chr1:171216672-171216722	HPAEpiC	pulmonary alveolar:	n/a
18	chr1:171216672-171216722	HAEpiC	amniotic membrane:	n/a
19	chr1:171216672-171216722	SK-N-SH	brain:	n/a
20	chr1:171216672-171216722	LNCaP	prostate:	n/a
21	chr1:171216672-171216722	HMEC	breast:	n/a
22	chr1:171216672-171216722	HCT-116	colon:	n/a
23	chr1:171216672-171216722	ProgFib	skin:	n/a
24	chr1:171216672-171216722	SKMC	muscle:	n/a
25	chr1:171216672-171216722	U87	brain:	n/a
26	chr1:171216672-171216722	GM06990	blood:	n/a
27	chr1:171216672-171216722	NT2-D1	testis:	n/a
28	chr1:171216672-171216722	PFSK-1	brain:	n/a
29	chr1:171216672-171216722	NHDF-neo	bronchial:	n/a
30	chr1:171216672-171216722	AG04450	lung:	fetal
31	chr1:171216672-171216722	HCM	heart:	n/a
32	chr1:171216672-171216722	Hepatocyte	liver:	n/a
33	chr1:171216672-171216722	HepG2	liver:	n/a
34	chr1:171216672-171216722	HUVEC	blood vessel:	n/a
35	chr1:171216672-171216722	A549	lung:	n/a
36	chr1:171216672-171216722	ECC-1	luminal epithelium:	n/a
37	chr1:171216672-171216722	GM12891	blood:	n/a
38	chr1:171216672-171216722	AG09319	gingival:	n/a
39	chr1:171216672-171216722	HCPEpiC	choroid plexus:	n/a
40	chr1:171216672-171216722	SK-N-SH_RA	brain:	n/a
41	chr1:171216672-171216722	BJ	skin:	n/a
42	chr1:171216672-171216722	T-47D	breast:	n/a
43	chr1:171216672-171216722	K562	blood:	n/a
44	chr1:171216672-171216722	NH-A	brain:	n/a
45	chr1:171216672-171216722	BE2_C	brain:	n/a
46	chr1:171216672-171216722	NB4	blood:	n/a
47	chr1:171216672-171216722	HNPCEpiC	eye:	n/a
48	chr1:171216672-171216722	MCF10A-Er-Src	breast:	n/a
49	chr1:171216672-171216722	SAEC	small airway:	n/a
50	chr1:171216672-171216722	MCF-7	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171215395..171216956-chr1:171219667..171221307,2	MCF-7	breast:
2	chr1:171216177..171217237-chr1:171282875..171283514,3	MCF-7	breast:

No data

Variant related genes	Relation type
FMO1	CpG island
ENSG00000231424	Chromatin interaction
ENSG00000076258	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10157270	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489230	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798240	0.85[ASN][1000 genomes]
rs10798252	0.89[ASN][1000 genomes]
rs10798253	0.92[ASN][1000 genomes]
rs10912475	0.85[ASN][1000 genomes]
rs10912529	0.91[ASN][1000 genomes]
rs10912542	0.93[ASN][1000 genomes]
rs11806072	0.89[ASN][1000 genomes]
rs12069067	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12078953	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080576	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12090485	0.96[ASN][1000 genomes]
rs12133385	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12405613	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567956	0.90[ASN][1000 genomes]
rs12730305	0.91[ASN][1000 genomes]
rs17350523	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1989656	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008706	0.85[ASN][1000 genomes]
rs2049922	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064078	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075987	0.93[ASN][1000 genomes]
rs2075990	0.94[ASN][1000 genomes]
rs2075991	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179105	0.94[ASN][1000 genomes]
rs2205723	0.93[ASN][1000 genomes]
rs2205727	0.96[ASN][1000 genomes]
rs2205728	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2205729	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2223228	0.91[ASN][1000 genomes]
rs2223232	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236874	0.92[ASN][1000 genomes]
rs2421709	0.89[ASN][1000 genomes]
rs2421710	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421711	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35152982	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738813	0.97[ASN][1000 genomes]
rs3754494	0.86[ASN][1000 genomes]
rs3768570	0.89[ASN][1000 genomes]
rs4480395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916182	0.93[ASN][1000 genomes]
rs4916191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916192	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425394	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425413	0.97[ASN][1000 genomes]
rs6657314	0.89[ASN][1000 genomes]
rs6672029	0.95[ASN][1000 genomes]
rs6692260	0.93[ASN][1000 genomes]
rs6699803	0.93[ASN][1000 genomes]
rs6701076	0.96[ASN][1000 genomes]
rs6703439	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7513485	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524635	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525342	0.85[ASN][1000 genomes]
rs7529080	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7531713	0.93[ASN][1000 genomes]
rs7531971	0.96[ASN][1000 genomes]
rs7536822	0.97[ASN][1000 genomes]
rs7538013	0.91[ASN][1000 genomes]
rs7545923	0.85[ASN][1000 genomes]
rs7553869	0.95[ASN][1000 genomes]
rs7887505	0.81[ASN][1000 genomes]
rs926268	0.86[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7520777	RP1-127D3.4	cis	Artery Tibial	GTEx
rs7520777	FMO2	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171200800-171220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:171211400-171218400	Weak transcription	Fetal Lung	lung
3	chr1:171214800-171216800	Weak transcription	Aorta	Aorta
4	chr1:171215800-171220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:171216000-171220000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:171216400-171217600	Enhancers	Fetal Intestine Large	intestine
7	chr1:171216600-171216800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:171216600-171217000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:171216600-171217600	Enhancers	Fetal Intestine Small	intestine

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