Variant report

Variant	rs16907555
Chromosome Location	chr10:57389340-57389341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:57389299-57389997	A549	lung:	n/a	chr10:57389621-57389634
2	CTCF	chr10:57389203-57391556	SK-N-SH	brain:	n/a	chr10:57391216-57391229 chr10:57391108-57391121 chr10:57389621-57389634 chr10:57391240-57391248
3	RAD21	chr10:57389028-57390218	SK-N-SH	brain:	n/a	n/a
4	SMC3	chr10:57389288-57389954	SK-N-SH	brain:	n/a	chr10:57389621-57389635
5	RFX5	chr10:57387421-57391674	SK-N-SH	brain:	n/a	chr10:57389894-57389902
6	CTCF	chr10:57389280-57389430	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr10:57389220-57389370	GM12872	blood:	n/a	n/a
8	NRF1	chr10:57389157-57389995	SK-N-SH	brain:	n/a	chr10:57389671-57389685

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:57389301-57389351	HIPEpiC	eye:	n/a
2	chr10:57389301-57389351	HCT-116	colon:	n/a
3	chr10:57389301-57389351	ovcar-3	ovarian:	n/a
4	chr10:57389301-57389351	HCM	heart:	n/a
5	chr10:57389301-57389351	HUVEC	blood vessel:	n/a
6	chr10:57389301-57389351	HPAEpiC	pulmonary alveolar:	n/a
7	chr10:57389301-57389351	GM12892	blood:	n/a
8	chr10:57389301-57389351	Caco-2	colon:	n/a
9	chr10:57389301-57389351	MCF-7	breast:	n/a
10	chr10:57389301-57389351	HCF	heart:	n/a
11	chr10:57389301-57389351	AoSMC	blood vessel:	n/a
12	chr10:57389301-57389351	HCPEpiC	choroid plexus:	n/a
13	chr10:57389301-57389351	HRE	kidney:	n/a
14	chr10:57389301-57389351	HL-60	blood:	n/a
15	chr10:57389301-57389351	NB4	blood:	n/a
16	chr10:57389301-57389351	ECC-1	luminal epithelium:	n/a
17	chr10:57389301-57389351	GM06990	blood:	n/a
18	chr10:57389301-57389351	PFSK-1	brain:	n/a
19	chr10:57389301-57389351	PrEC	prostate:	n/a
20	chr10:57389301-57389351	ProgFib	skin:	n/a
21	chr10:57389301-57389351	AG09319	gingival:	n/a
22	chr10:57389301-57389351	GM19239	blood:	n/a
23	chr10:57389301-57389351	HEK293	kidney:	embryo
24	chr10:57389301-57389351	A549	lung:	n/a
25	chr10:57389301-57389351	NHBE	bronchial:	n/a
26	chr10:57389301-57389351	NH-A	brain:	n/a
27	chr10:57389301-57389351	BE2_C	brain:	n/a
28	chr10:57389301-57389351	AG04449	skin:	fetal
29	chr10:57389301-57389351	HRPEpiC	eye:	n/a
30	chr10:57389301-57389351	MCF10A-Er-Src	breast:	n/a
31	chr10:57389301-57389351	HepG2	liver:	n/a
32	chr10:57389301-57389351	CMK	blood:	n/a
33	chr10:57389301-57389351	HEEpiC	esophagus:	n/a
34	chr10:57389301-57389351	H1-hESC	embryonic stem cell:	embryo
35	chr10:57389301-57389351	SK-N-SH_RA	brain:	n/a
36	chr10:57389301-57389351	T-47D	breast:	n/a
37	chr10:57389301-57389351	Hela-S3	cervix:	n/a
38	chr10:57389301-57389351	U87	brain:	n/a
39	chr10:57389301-57389351	HMEC	breast:	n/a
40	chr10:57389301-57389351	HAEpiC	amniotic membrane:	n/a
41	chr10:57389301-57389351	RPTEC	kidney:	n/a
42	chr10:57389301-57389351	Jurkat	blood:	n/a
43	chr10:57389301-57389351	HRCEpiC	kidney:	n/a
44	chr10:57389301-57389351	IMR90	lung:	fetal
45	chr10:57389301-57389351	Hepatocyte	liver:	n/a
46	chr10:57389301-57389351	SK-N-SH	brain:	n/a
47	chr10:57389301-57389351	NT2-D1	testis:	n/a
48	chr10:57389301-57389351	SAEC	small airway:	n/a
49	chr10:57389301-57389351	AG10803	skin:	n/a
50	chr10:57389301-57389351	BJ	skin:	n/a

No data

Variant related genes	Relation type
PCDH15	TF binding region
PCDH15	CpG island

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12412060	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16915045	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916525	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2461905	0.98[ASN][1000 genomes]
rs4130563	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59870719	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59899587	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60003158	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60987822	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039099	chr10:56984902-57394831	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv540641	chr10:56984902-57394831	Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1040047	chr10:57007182-57979747	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv895480	chr10:57120283-57539172	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1046216	chr10:57132407-57470412	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv2761598	chr10:57143239-57656115	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1040346	chr10:57166917-57410348	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv993479	chr10:57187055-57404999	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv895482	chr10:57213026-57476292	Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1053051	chr10:57252816-57638793	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1053015	chr10:57304437-57467168	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1041500	chr10:57317208-57638793	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv895484	chr10:57323162-57389340	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv895485	chr10:57323162-57431871	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv895486	chr10:57323162-57476292	Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1048800	chr10:57333479-57430517	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv895487	chr10:57335764-57476292	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv895488	chr10:57345779-57401749	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv551045	chr10:57351781-57442129	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv895489	chr10:57354709-57420417	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv1048148	chr10:57359414-57498605	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv428558	chr10:57383256-57524282	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:57388400-57389600	Weak transcription	Pancreas	Pancrea
2	chr10:57388400-57390000	Weak transcription	Gastric	stomach
3	chr10:57388600-57389600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:57388600-57389600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:57388600-57389600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:57388600-57389600	Weak transcription	Right Atrium	heart
7	chr10:57388600-57390200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:57388800-57389600	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links