Variant report

Variant	rs3851306
Chromosome Location	chr1:242120953-242120954
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:1)
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	chr1:242120907-242120957	HNPCEpiC	eye:	n/a
2	chr1:242120907-242120957	AG09309	skin:	n/a
3	chr1:242120907-242120957	LNCaP	prostate:	n/a
4	chr1:242120907-242120957	AoSMC	blood vessel:	n/a
5	chr1:242120907-242120957	BJ	skin:	n/a
6	chr1:242120907-242120957	GM12878	blood:	n/a
7	chr1:242120907-242120957	HEEpiC	esophagus:	n/a
8	chr1:242120907-242120957	HIPEpiC	eye:	n/a
9	chr1:242120907-242120957	GM12891	blood:	n/a
10	chr1:242120907-242120957	MCF-7	breast:	n/a
11	chr1:242120907-242120957	Hepatocyte	liver:	n/a
12	chr1:242120907-242120957	SK-N-SH_RA	brain:	n/a
13	chr1:242120907-242120957	PANC-1	pancreas:	n/a
14	chr1:242120907-242120957	SKMC	muscle:	n/a
15	chr1:242120907-242120957	T-47D	breast:	n/a
16	chr1:242120907-242120957	HRE	kidney:	n/a
17	chr1:242120907-242120957	IMR90	lung:	fetal
18	chr1:242120907-242120957	GM06990	blood:	n/a
19	chr1:242120907-242120957	BE2_C	brain:	n/a
20	chr1:242120907-242120957	HL-60	blood:	n/a
21	chr1:242120907-242120957	RPTEC	kidney:	n/a
22	chr1:242120907-242120957	A549	lung:	n/a
23	chr1:242120907-242120957	SK-N-SH	brain:	n/a
24	chr1:242120907-242120957	HMEC	breast:	n/a
25	chr1:242120907-242120957	PFSK-1	brain:	n/a
26	chr1:242120907-242120957	HCM	heart:	n/a
27	chr1:242120907-242120957	U87	brain:	n/a
28	chr1:242120907-242120957	Hela-S3	cervix:	n/a
29	chr1:242120907-242120957	HCPEpiC	choroid plexus:	n/a
30	chr1:242120907-242120957	NH-A	brain:	n/a
31	chr1:242120907-242120957	HAEpiC	amniotic membrane:	n/a
32	chr1:242120907-242120957	HEK293	kidney:	embryo
33	chr1:242120907-242120957	NT2-D1	testis:	n/a
34	chr1:242120907-242120957	AG09319	gingival:	n/a
35	chr1:242120907-242120957	NHBE	bronchial:	n/a
36	chr1:242120907-242120957	CMK	blood:	n/a
37	chr1:242120907-242120957	Caco-2	colon:	n/a
38	chr1:242120907-242120957	SK-N-MC	brain:	n/a
39	chr1:242120907-242120957	AG04450	lung:	fetal
40	chr1:242120907-242120957	HRCEpiC	kidney:	n/a
41	chr1:242120907-242120957	ECC-1	luminal epithelium:	n/a
42	chr1:242120907-242120957	ProgFib	skin:	n/a
43	chr1:242120907-242120957	HCF	heart:	n/a
44	chr1:242120907-242120957	HepG2	liver:	n/a
45	chr1:242120907-242120957	NHDF-neo	bronchial:	n/a
46	chr1:242120907-242120957	GM12892	blood:	n/a
47	chr1:242120907-242120957	HUVEC	blood vessel:	n/a
48	chr1:242120907-242120957	SAEC	small airway:	n/a
49	chr1:242120907-242120957	AG10803	skin:	n/a
50	chr1:242120907-242120957	GM19239	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:242120814..242121654-chr1:242161517..242162480,3	MCF-7	breast:

No data

Variant related genes	Relation type
BECN1P1	CpG island
ENSG00000197769	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28385880	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28392846	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28413917	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28438742	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28439042	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28444922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28472777	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28544076	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28615546	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28624657	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28626680	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28656906	0.80[ASN][1000 genomes]
rs28661887	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28662297	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28662847	0.88[EUR][1000 genomes]
rs28698435	0.83[ASN][1000 genomes]
rs28710235	0.90[EUR][1000 genomes]
rs28718445	0.88[EUR][1000 genomes]
rs34212793	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34518223	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34652934	0.90[EUR][1000 genomes]
rs34735536	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35027076	0.90[EUR][1000 genomes]
rs35341580	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35363238	0.84[EUR][1000 genomes]
rs35454394	0.86[EUR][1000 genomes]
rs35524854	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35536186	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35892843	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35896847	0.82[ASN][1000 genomes]
rs36083518	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851304	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851305	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851307	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3862974	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3862975	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3915586	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56335758	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59504163	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60043862	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66861684	0.91[EUR][1000 genomes]
rs67802349	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs695234	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs695235	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71535345	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71648675	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72757276	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72757280	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs955535	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1008886	chr1:242015591-242176983	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2750830	chr1:242025098-242303357	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv2750831	chr1:242025098-242332959	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1002309	chr1:242042242-242295635	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv870442	chr1:242105882-242136576	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv947475	chr1:242119659-242136347	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:242114000-242121200	Weak transcription	Fetal Muscle Leg	muscle

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