Variant report

Variant	rs3749690
Chromosome Location	chr5:147693826-147693827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:147693820-147693970	HMEC	breast:	n/a	n/a
2	CTCF	chr5:147693800-147693950	MCF-7	breast:	n/a	n/a
3	CEBPB	chr5:147693767-147694117	HepG2	liver:	n/a	chr5:147693935-147693946
4	RAD21	chr5:147693812-147694044	SK-N-SH_RA	brain:	n/a	n/a
5	RAD21	chr5:147693691-147694157	MCF-7	breast:	n/a	n/a
6	CTCF	chr5:147693760-147693910	NHEK	skin:	n/a	n/a
7	RAD21	chr5:147693711-147694080	MCF-7	breast:	n/a	n/a
8	CTCF	chr5:147693800-147693950	SAEC	small airway:	n/a	n/a
9	CTCF	chr5:147693777-147694062	K562	blood:	n/a	n/a
10	CTCF	chr5:147693685-147694178	HCT-116	colon:	n/a	n/a
11	CEBPB	chr5:147693747-147694128	K562	blood:	n/a	chr5:147693935-147693946
12	MYC	chr5:147693793-147694078	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr5:147693820-147693970	HepG2	liver:	n/a	n/a
14	RAD21	chr5:147693715-147694123	HCT-116	colon:	n/a	n/a
15	RAD21	chr5:147693752-147694105	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr5:147693674-147694243	HCT-116	colon:	n/a	chr5:147693935-147693946
17	FOS	chr5:147693824-147694053	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr5:147693642-147694148	HCT-116	colon:	n/a	n/a
19	CTCF	chr5:147693764-147694166	MCF-7	breast:	n/a	n/a
20	CTCF	chr5:147693760-147693910	Caco-2	colon:	n/a	n/a
21	CTCF	chr5:147693800-147693950	HRE	kidney:	n/a	n/a
22	CEBPB	chr5:147693709-147694233	MCF-7	breast:	n/a	chr5:147693935-147693946
23	CEBPB	chr5:147693814-147694035	H1-hESC	embryonic stem cell:	n/a	chr5:147693935-147693946
24	CTCF	chr5:147693815-147694061	MCF-7	breast:	n/a	n/a
25	CTCF	chr5:147693680-147693830	GM12875	blood:	n/a	n/a
26	CEBPB	chr5:147693824-147694081	IMR90	lung:	n/a	chr5:147693935-147693946
27	CEBPB	chr5:147693752-147694130	Hela-S3	cervix:	n/a	chr5:147693935-147693946
28	CTCF	chr5:147693707-147694150	MCF-7	breast:	n/a	n/a
29	CEBPB	chr5:147693770-147694061	K562	blood:	n/a	chr5:147693935-147693946
30	CTCF	chr5:147693680-147693830	RPTEC	kidney:	n/a	n/a
31	CEBPB	chr5:147693771-147694106	A549	lung:	n/a	chr5:147693935-147693946
32	FOS	chr5:147693824-147694075	MCF10A-Er-Src	breast:	n/a	n/a
33	CEBPB	chr5:147693674-147694173	MCF-7	breast:	n/a	chr5:147693935-147693946
34	SMC3	chr5:147693781-147694128	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:147693779-147693829	ovcar-3	ovarian:	n/a
2	chr5:147693779-147693829	SK-N-SH_RA	brain:	n/a
3	chr5:147693779-147693829	GM12891	blood:	n/a
4	chr5:147693779-147693829	HIPEpiC	eye:	n/a
5	chr5:147693779-147693829	A549	lung:	n/a
6	chr5:147693779-147693829	HL-60	blood:	n/a
7	chr5:147693779-147693829	HEEpiC	esophagus:	n/a
8	chr5:147693779-147693829	SKMC	muscle:	n/a
9	chr5:147693779-147693829	HMEC	breast:	n/a
10	chr5:147693779-147693829	AG10803	skin:	n/a
11	chr5:147693779-147693829	HCM	heart:	n/a
12	chr5:147693779-147693829	AG09319	gingival:	n/a
13	chr5:147693779-147693829	ProgFib	skin:	n/a
14	chr5:147693779-147693829	H1-hESC	embryonic stem cell:	embryo
15	chr5:147693779-147693829	IMR90	lung:	fetal
16	chr5:147693779-147693829	MCF-7	breast:	n/a
17	chr5:147693779-147693829	BJ	skin:	n/a
18	chr5:147693779-147693829	HUVEC	blood vessel:	n/a
19	chr5:147693779-147693829	HAEpiC	amniotic membrane:	n/a
20	chr5:147693779-147693829	HNPCEpiC	eye:	n/a
21	chr5:147693779-147693829	GM12892	blood:	n/a
22	chr5:147693779-147693829	PANC-1	pancreas:	n/a
23	chr5:147693779-147693829	AG04450	lung:	fetal
24	chr5:147693779-147693829	LNCaP	prostate:	n/a
25	chr5:147693779-147693829	HPAEpiC	pulmonary alveolar:	n/a
26	chr5:147693779-147693829	AG04449	skin:	fetal
27	chr5:147693779-147693829	PFSK-1	brain:	n/a
28	chr5:147693779-147693829	NHDF-neo	bronchial:	n/a
29	chr5:147693779-147693829	NH-A	brain:	n/a
30	chr5:147693779-147693829	HRCEpiC	kidney:	n/a
31	chr5:147693779-147693829	SK-N-SH	brain:	n/a
32	chr5:147693779-147693829	ECC-1	luminal epithelium:	n/a
33	chr5:147693779-147693829	HRPEpiC	eye:	n/a
34	chr5:147693779-147693829	NT2-D1	testis:	n/a
35	chr5:147693779-147693829	Hepatocyte	liver:	n/a
36	chr5:147693779-147693829	T-47D	breast:	n/a
37	chr5:147693779-147693829	SAEC	small airway:	n/a
38	chr5:147693779-147693829	GM19239	blood:	n/a
39	chr5:147693779-147693829	Jurkat	blood:	n/a
40	chr5:147693779-147693829	Caco-2	colon:	n/a
41	chr5:147693779-147693829	BE2_C	brain:	n/a
42	chr5:147693779-147693829	HEK293	kidney:	embryo
43	chr5:147693779-147693829	NHBE	bronchial:	n/a
44	chr5:147693779-147693829	HCPEpiC	choroid plexus:	n/a
45	chr5:147693779-147693829	Hela-S3	cervix:	n/a
46	chr5:147693779-147693829	MCF10A-Er-Src	breast:	n/a
47	chr5:147693779-147693829	PrEC	prostate:	n/a
48	chr5:147693779-147693829	GM06990	blood:	n/a
49	chr5:147693779-147693829	AoSMC	blood vessel:	n/a
50	chr5:147693779-147693829	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147693682..147694524-chr5:147754020..147754809,2	MCF-7	breast:
2	chr5:147692078..147693866-chr5:147761440..147764078,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPINK7-1	chr5:147692937-147694042	NONHSAT104444
2	lnc-SPINK7-1	chr5:147693663-147694071	NONHSAT104445

No data

Variant related genes	Relation type
ENSG00000268126	TF binding region
ENSG00000268126	CpG island
ENSG00000247199	Chromatin interaction
ENSG00000145868	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10036053	0.95[EUR][1000 genomes]
rs10037318	0.89[EUR][1000 genomes]
rs10044054	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050560	0.89[ASW][hapmap];0.83[CEU][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10057472	0.90[EUR][1000 genomes]
rs10060180	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10060753	0.80[CEU][hapmap]
rs10068891	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072817	0.93[EUR][1000 genomes]
rs10072958	0.95[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10077690	0.80[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs10476892	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477374	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515610	0.89[EUR][1000 genomes]
rs12516267	0.91[EUR][1000 genomes]
rs12519039	0.90[EUR][1000 genomes]
rs12521065	0.95[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12717971	0.92[EUR][1000 genomes]
rs12717973	0.80[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs13153619	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157347	0.93[EUR][1000 genomes]
rs13158948	0.89[EUR][1000 genomes]
rs13176114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358385	0.90[EUR][1000 genomes]
rs1345741	0.86[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1363704	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1363705	0.89[EUR][1000 genomes]
rs1363707	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs1422968	0.92[EUR][1000 genomes]
rs1422970	0.92[EUR][1000 genomes]
rs1422976	0.90[CEU][hapmap]
rs1422977	0.83[EUR][1000 genomes]
rs1582519	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs17719578	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719662	0.95[EUR][1000 genomes]
rs17719763	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17719873	0.92[EUR][1000 genomes]
rs17776554	0.90[EUR][1000 genomes]
rs17776674	0.90[EUR][1000 genomes]
rs1862430	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862431	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2161432	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216653	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400509	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400510	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28442279	0.90[EUR][1000 genomes]
rs2895761	0.92[EUR][1000 genomes]
rs34001290	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34163281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35006442	0.86[EUR][1000 genomes]
rs35700061	0.92[EUR][1000 genomes]
rs35792476	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749689	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs4406123	0.83[EUR][1000 genomes]
rs4705247	0.86[CEU][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4705248	0.95[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4705249	0.90[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4705251	0.90[EUR][1000 genomes]
rs4705252	0.90[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs6580542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580544	0.93[EUR][1000 genomes]
rs6580545	0.95[CEU][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs6580546	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs6580548	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860261	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6865036	0.85[EUR][1000 genomes]
rs6865972	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866106	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875795	0.90[EUR][1000 genomes]
rs6876308	0.90[EUR][1000 genomes]
rs6876982	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6882932	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886203	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6891724	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892647	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs6893378	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712350	0.90[EUR][1000 genomes]
rs7713986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716578	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722458	0.89[EUR][1000 genomes]
rs7729309	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs7730707	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7731526	0.90[EUR][1000 genomes]
rs7734458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736728	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325094	0.89[EUR][1000 genomes]
rs9784645	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999741	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv599945	chr5:147649181-147720487	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv965612	chr5:147692551-147695193	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3749690	SPINK9	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147687800-147694000	Weak transcription	Fetal Heart	heart
2	chr5:147689000-147699600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:147693600-147694200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:147693600-147695000	Enhancers	Right Atrium	heart
5	chr5:147693800-147694200	Enhancers	Left Ventricle	heart
6	chr5:147693800-147695200	Enhancers	Fetal Brain Male	brain
7	chr5:147693800-147699600	Weak transcription	Esophagus	oesophagus

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