Variant report

Variant	rs539897
Chromosome Location	chr3:191178925-191178926
allele	C/T
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	chr3:191178924-191178974	AG09319	gingival:	n/a
2	chr3:191178924-191178974	HL-60	blood:	n/a
3	chr3:191178924-191178974	Hela-S3	cervix:	n/a
4	chr3:191178924-191178974	Caco-2	colon:	n/a
5	chr3:191178924-191178974	K562	blood:	n/a
6	chr3:191178924-191178974	HRCEpiC	kidney:	n/a
7	chr3:191178924-191178974	Hepatocyte	liver:	n/a
8	chr3:191178924-191178974	SK-N-SH_RA	brain:	n/a
9	chr3:191178924-191178974	H1-hESC	embryonic stem cell:	embryo
10	chr3:191178924-191178974	AG04450	lung:	fetal
11	chr3:191178924-191178974	HepG2	liver:	n/a
12	chr3:191178924-191178974	HAEpiC	amniotic membrane:	n/a
13	chr3:191178924-191178974	CMK	blood:	n/a
14	chr3:191178924-191178974	NT2-D1	testis:	n/a
15	chr3:191178924-191178974	NH-A	brain:	n/a
16	chr3:191178924-191178974	U87	brain:	n/a
17	chr3:191178924-191178974	LNCaP	prostate:	n/a
18	chr3:191178924-191178974	Jurkat	blood:	n/a
19	chr3:191178924-191178974	HCM	heart:	n/a
20	chr3:191178924-191178974	MCF10A-Er-Src	breast:	n/a
21	chr3:191178924-191178974	AG09309	skin:	n/a
22	chr3:191178924-191178974	PANC-1	pancreas:	n/a
23	chr3:191178924-191178974	HPAEpiC	pulmonary alveolar:	n/a
24	chr3:191178924-191178974	HEK293	kidney:	embryo
25	chr3:191178924-191178974	ProgFib	skin:	n/a
26	chr3:191178924-191178974	PrEC	prostate:	n/a
27	chr3:191178924-191178974	HCT-116	colon:	n/a
28	chr3:191178924-191178974	SAEC	small airway:	n/a
29	chr3:191178924-191178974	NB4	blood:	n/a
30	chr3:191178924-191178974	PFSK-1	brain:	n/a
31	chr3:191178924-191178974	HIPEpiC	eye:	n/a
32	chr3:191178924-191178974	NHDF-neo	bronchial:	n/a
33	chr3:191178924-191178974	AoSMC	blood vessel:	n/a
34	chr3:191178924-191178974	ovcar-3	ovarian:	n/a
35	chr3:191178924-191178974	SK-N-MC	brain:	n/a
36	chr3:191178924-191178974	GM19239	blood:	n/a
37	chr3:191178924-191178974	GM12878	blood:	n/a
38	chr3:191178924-191178974	AG10803	skin:	n/a
39	chr3:191178924-191178974	AG04449	skin:	fetal
40	chr3:191178924-191178974	HUVEC	blood vessel:	n/a
41	chr3:191178924-191178974	BE2_C	brain:	n/a
42	chr3:191178924-191178974	A549	lung:	n/a
43	chr3:191178924-191178974	HNPCEpiC	eye:	n/a
44	chr3:191178924-191178974	BJ	skin:	n/a
45	chr3:191178924-191178974	MCF-7	breast:	n/a
46	chr3:191178924-191178974	HCPEpiC	choroid plexus:	n/a
47	chr3:191178924-191178974	HCF	heart:	n/a
48	chr3:191178924-191178974	SKMC	muscle:	n/a
49	chr3:191178924-191178974	IMR90	lung:	fetal
50	chr3:191178924-191178974	HRE	kidney:	n/a

No data

Variant related genes	Relation type
PYDC2	CpG island

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1066868	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159487	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs167149	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192672	0.80[ASN][1000 genomes]
rs293821	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs293835	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399285	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs411677	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs448224	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs452735	0.91[ASN][1000 genomes]
rs518974	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs542592	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs550972	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564560	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695957	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs695960	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697917	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782037	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3432654	chr3:191161299-191183570	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv878108	chr3:191175215-191223664	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv878109	chr3:191178925-191227296	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs539897	PYDC2	cis	parietal	SCAN
rs539897	UTS2D	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191175400-191190200	Weak transcription	K562	blood

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