Variant report

Variant	rs3802306
Chromosome Location	chr8:3253997-3253998
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: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	chr8:3253958-3254008	GM06990	blood:	n/a
2	chr8:3253958-3254008	T-47D	breast:	n/a
3	chr8:3253958-3254008	NHBE	bronchial:	n/a
4	chr8:3253958-3254008	HAEpiC	amniotic membrane:	n/a
5	chr8:3253958-3254008	ovcar-3	ovarian:	n/a
6	chr8:3253958-3254008	AoSMC	blood vessel:	n/a
7	chr8:3253958-3254008	NHDF-neo	bronchial:	n/a
8	chr8:3253958-3254008	Hepatocyte	liver:	n/a
9	chr8:3253958-3254008	AG09319	gingival:	n/a
10	chr8:3253958-3254008	PFSK-1	brain:	n/a
11	chr8:3253958-3254008	SK-N-MC	brain:	n/a
12	chr8:3253958-3254008	LNCaP	prostate:	n/a
13	chr8:3253958-3254008	ProgFib	skin:	n/a
14	chr8:3253958-3254008	SK-N-SH	brain:	n/a
15	chr8:3253958-3254008	IMR90	lung:	fetal
16	chr8:3253958-3254008	AG09309	skin:	n/a
17	chr8:3253958-3254008	NB4	blood:	n/a
18	chr8:3253958-3254008	HIPEpiC	eye:	n/a
19	chr8:3253958-3254008	HCPEpiC	choroid plexus:	n/a
20	chr8:3253958-3254008	SAEC	small airway:	n/a
21	chr8:3253958-3254008	MCF10A-Er-Src	breast:	n/a
22	chr8:3253958-3254008	GM19239	blood:	n/a
23	chr8:3253958-3254008	HL-60	blood:	n/a
24	chr8:3253958-3254008	Hela-S3	cervix:	n/a
25	chr8:3253958-3254008	K562	blood:	n/a
26	chr8:3253958-3254008	SK-N-SH_RA	brain:	n/a
27	chr8:3253958-3254008	BJ	skin:	n/a
28	chr8:3253958-3254008	HepG2	liver:	n/a
29	chr8:3253958-3254008	HRPEpiC	eye:	n/a
30	chr8:3253958-3254008	BE2_C	brain:	n/a
31	chr8:3253958-3254008	CMK	blood:	n/a
32	chr8:3253958-3254008	GM12892	blood:	n/a
33	chr8:3253958-3254008	AG10803	skin:	n/a
34	chr8:3253958-3254008	HPAEpiC	pulmonary alveolar:	n/a
35	chr8:3253958-3254008	HNPCEpiC	eye:	n/a
36	chr8:3253958-3254008	HCF	heart:	n/a
37	chr8:3253958-3254008	HCM	heart:	n/a
38	chr8:3253958-3254008	SKMC	muscle:	n/a
39	chr8:3253958-3254008	H1-hESC	embryonic stem cell:	embryo
40	chr8:3253958-3254008	HRE	kidney:	n/a
41	chr8:3253958-3254008	HRCEpiC	kidney:	n/a
42	chr8:3253958-3254008	NT2-D1	testis:	n/a
43	chr8:3253958-3254008	AG04449	skin:	fetal
44	chr8:3253958-3254008	Jurkat	blood:	n/a
45	chr8:3253958-3254008	HMEC	breast:	n/a
46	chr8:3253958-3254008	PrEC	prostate:	n/a
47	chr8:3253958-3254008	ECC-1	luminal epithelium:	n/a
48	chr8:3253958-3254008	HEK293	kidney:	embryo
49	chr8:3253958-3254008	HCT-116	colon:	n/a
50	chr8:3253958-3254008	HUVEC	blood vessel:	n/a

No data

Variant related genes	Relation type
CSMD1	CpG island

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1039491	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1039492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1039493	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11136620	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11136621	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11136622	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11775235	0.96[CEU][hapmap];0.82[GIH][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1178231	0.98[GIH][hapmap];0.83[JPT][hapmap]
rs12375250	0.89[ASN][1000 genomes]
rs12375425	0.90[ASN][1000 genomes]
rs12543118	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12543159	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12544077	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12545711	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12681614	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13253365	0.91[EUR][1000 genomes]
rs13275230	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1447358	0.85[ASN][1000 genomes]
rs1979830	0.88[JPT][hapmap]
rs1995231	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166710	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708682	0.87[ASN][1000 genomes]
rs3802304	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3802305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495450	0.84[ASN][1000 genomes]
rs5023366	0.88[JPT][hapmap]
rs57298419	0.85[ASN][1000 genomes]
rs6990498	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6993217	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7001593	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7005990	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7006193	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs7007789	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7014229	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7018302	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7815237	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7815361	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7841495	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7844978	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9969437	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9969438	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9969441	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9969528	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs9969535	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9969537	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9969557	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs9969619	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9969646	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033589	chr8:2498609-3305100	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018407	chr8:2724294-3305100	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv915568	chr8:2725834-3291312	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1025408	chr8:2733604-3302447	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1025209	chr8:3067655-3754882	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1026643	chr8:3077210-3277827	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1026998	chr8:3102679-3593264	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv889896	chr8:3165777-3262931	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1034076	chr8:3168033-3989947	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv539351	chr8:3168033-3989947	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1017164	chr8:3174168-4026811	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv539352	chr8:3174168-4026811	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1018218	chr8:3180287-4089011	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3802306	FBXO25	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:3243400-3256400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:3253600-3254800	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr8:3253800-3254800	Weak transcription	Brain Angular Gyrus	brain

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