Variant report

Variant	rs12040837
Chromosome Location	chr1:153068267-153068268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:153068163-153068663	K562	blood:	n/a	n/a
2	GATA2	chr1:153068166-153068695	HUVEC	blood vessel:	n/a	chr1:153068346-153068356 chr1:153068347-153068354 chr1:153068347-153068354 chr1:153068347-153068354

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153068236-153068286	SAEC	small airway:	n/a
2	chr1:153068231-153068281	PFSK-1	brain:	n/a
3	chr1:153068231-153068281	AG04450	lung:	fetal
4	chr1:153068231-153068281	ProgFib	skin:	n/a
5	chr1:153068231-153068281	SKMC	muscle:	n/a
6	chr1:153068231-153068281	HCPEpiC	choroid plexus:	n/a
7	chr1:153068231-153068281	NB4	blood:	n/a
8	chr1:153068236-153068286	AG09319	gingival:	n/a
9	chr1:153068231-153068281	SAEC	small airway:	n/a
10	chr1:153068236-153068286	A549	lung:	n/a
11	chr1:153068236-153068286	MCF10A-Er-Src	breast:	n/a
12	chr1:153068231-153068281	NT2-D1	testis:	n/a
13	chr1:153068236-153068286	HEEpiC	esophagus:	n/a
14	chr1:153068236-153068286	ECC-1	luminal epithelium:	n/a
15	chr1:153068231-153068281	CMK	blood:	n/a
16	chr1:153068231-153068281	HAEpiC	amniotic membrane:	n/a
17	chr1:153068231-153068281	NHBE	bronchial:	n/a
18	chr1:153068236-153068286	IMR90	lung:	fetal
19	chr1:153068236-153068286	HRE	kidney:	n/a
20	chr1:153068236-153068286	CMK	blood:	n/a
21	chr1:153068231-153068281	SK-N-SH	brain:	n/a
22	chr1:153068231-153068281	HEEpiC	esophagus:	n/a
23	chr1:153068236-153068286	HL-60	blood:	n/a
24	chr1:153068231-153068281	GM06990	blood:	n/a
25	chr1:153068231-153068281	Caco-2	colon:	n/a
26	chr1:153068236-153068286	Hela-S3	cervix:	n/a
27	chr1:153068236-153068286	K562	blood:	n/a
28	chr1:153068231-153068281	K562	blood:	n/a
29	chr1:153068231-153068281	SK-N-SH_RA	brain:	n/a
30	chr1:153068231-153068281	T-47D	breast:	n/a
31	chr1:153068231-153068281	MCF-7	breast:	n/a
32	chr1:153068236-153068286	BJ	skin:	n/a
33	chr1:153068231-153068281	A549	lung:	n/a
34	chr1:153068231-153068281	HCF	heart:	n/a
35	chr1:153068236-153068286	NHBE	bronchial:	n/a
36	chr1:153068231-153068281	HUVEC	blood vessel:	n/a
37	chr1:153068236-153068286	HCT-116	colon:	n/a
38	chr1:153068236-153068286	MCF-7	breast:	n/a
39	chr1:153068231-153068281	ECC-1	luminal epithelium:	n/a
40	chr1:153068236-153068286	ovcar-3	ovarian:	n/a
41	chr1:153068231-153068281	MCF10A-Er-Src	breast:	n/a
42	chr1:153068236-153068286	NH-A	brain:	n/a
43	chr1:153068231-153068281	NHDF-neo	bronchial:	n/a
44	chr1:153068231-153068281	SK-N-MC	brain:	n/a
45	chr1:153068236-153068286	AoSMC	blood vessel:	n/a
46	chr1:153068236-153068286	AG09309	skin:	n/a
47	chr1:153068236-153068286	NHDF-neo	bronchial:	n/a
48	chr1:153068236-153068286	HIPEpiC	eye:	n/a
49	chr1:153068231-153068281	RPTEC	kidney:	n/a
50	chr1:153068236-153068286	GM06990	blood:	n/a

No data

Variant related genes	Relation type
SPRR2E	TF binding region
SPRR2E	CpG island

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10157591	0.84[AMR][1000 genomes]
rs1119652	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205197	1.00[ASN][1000 genomes]
rs11205205	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11205206	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11205207	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11205212	0.83[EUR][1000 genomes]
rs11205213	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12029300	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12032237	1.00[ASN][1000 genomes]
rs12035172	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12036590	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12037255	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12041391	1.00[ASN][1000 genomes]
rs12045045	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12406869	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12408875	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12409742	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12565377	0.94[ASN][1000 genomes]
rs12567386	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12735128	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13376230	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13376281	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1500940	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16834968	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16834971	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1926235	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2018193	0.94[ASN][1000 genomes]
rs2291979	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28609100	0.84[AMR][1000 genomes]
rs28664069	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs310131	1.00[ASN][1000 genomes]
rs3766532	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3843258	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3913438	1.00[ASN][1000 genomes]
rs55676349	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55780839	1.00[ASN][1000 genomes]
rs57115197	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58093379	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58339221	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58665653	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58809172	0.84[AMR][1000 genomes]
rs60509474	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60797518	0.82[AMR][1000 genomes]
rs61204539	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61315454	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs628724	1.00[ASN][1000 genomes]
rs6587728	0.83[ASN][1000 genomes]
rs6587730	0.97[ASN][1000 genomes]
rs6679633	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6692216	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72480208	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs735154	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74133286	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7520621	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7532449	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7534523	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7541753	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7541865	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7553750	0.94[ASN][1000 genomes]
rs904949	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv464017	chr1:153033406-153099345	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv547920	chr1:153033406-153099345	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv946395	chr1:153042430-153069958	Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3425721	chr1:153057079-153076073	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153055200-153068400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:153067400-153068400	Weak transcription	Hela-S3	cervix
3	chr1:153067400-153070200	Weak transcription	NHEK	skin
4	chr1:153067400-153072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:153068200-153069600	Enhancers	K562	blood

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