Variant report

Variant	rs10799364
Chromosome Location	chr1:223853971-223853972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:122)
Chromatin interactive
region (count:5)
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	FOS	chr1:223853309-223854025	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
2	FOS	chr1:223853309-223854343	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
3	STAT3	chr1:223853429-223854335	MCF10A-Er-Src	breast:	n/a	chr1:223854169-223854180
4	MYC	chr1:223853438-223854310	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:223853424-223854325	MCF10A-Er-Src	breast:	n/a	chr1:223854169-223854180
6	FOS	chr1:223853309-223854391	MCF10A-Er-Src	breast:	n/a	chr1:223853489-223853498 chr1:223853491-223853498 chr1:223853489-223853499 chr1:223853484-223853493
7	SIN3AK20	chr1:223853018-223853984	MCF-7	breast:	n/a	n/a
8	STAT3	chr1:223853408-223854347	MCF10A-Er-Src	breast:	n/a	chr1:223854169-223854180

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:223853928-223853978	HEEpiC	esophagus:	n/a
2	chr1:223853949-223853999	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:223853949-223853999	HepG2	liver:	n/a
4	chr1:223853949-223853999	GM19239	blood:	n/a
5	chr1:223853928-223853978	AG09319	gingival:	n/a
6	chr1:223853949-223853999	SK-N-SH	brain:	n/a
7	chr1:223853949-223853999	Hela-S3	cervix:	n/a
8	chr1:223853949-223853999	HRPEpiC	eye:	n/a
9	chr1:223853928-223853978	IMR90	lung:	fetal
10	chr1:223853928-223853978	AoSMC	blood vessel:	n/a
11	chr1:223853949-223853999	K562	blood:	n/a
12	chr1:223853928-223853978	LNCaP	prostate:	n/a
13	chr1:223853928-223853978	HPAEpiC	pulmonary alveolar:	n/a
14	chr1:223853949-223853999	ECC-1	luminal epithelium:	n/a
15	chr1:223853949-223853999	U87	brain:	n/a
16	chr1:223853928-223853978	U87	brain:	n/a
17	chr1:223853928-223853978	T-47D	breast:	n/a
18	chr1:223853928-223853978	H1-hESC	embryonic stem cell:	embryo
19	chr1:223853949-223853999	Caco-2	colon:	n/a
20	chr1:223853949-223853999	AG04450	lung:	fetal
21	chr1:223853928-223853978	GM12878	blood:	n/a
22	chr1:223853949-223853999	Hepatocyte	liver:	n/a
23	chr1:223853928-223853978	RPTEC	kidney:	n/a
24	chr1:223853928-223853978	AG04450	lung:	fetal
25	chr1:223853949-223853999	T-47D	breast:	n/a
26	chr1:223853928-223853978	HNPCEpiC	eye:	n/a
27	chr1:223853928-223853978	Hepatocyte	liver:	n/a
28	chr1:223853949-223853999	HL-60	blood:	n/a
29	chr1:223853949-223853999	A549	lung:	n/a
30	chr1:223853949-223853999	PFSK-1	brain:	n/a
31	chr1:223853949-223853999	LNCaP	prostate:	n/a
32	chr1:223853949-223853999	RPTEC	kidney:	n/a
33	chr1:223853949-223853999	AoSMC	blood vessel:	n/a
34	chr1:223853928-223853978	HAEpiC	amniotic membrane:	n/a
35	chr1:223853949-223853999	SK-N-MC	brain:	n/a
36	chr1:223853949-223853999	HEEpiC	esophagus:	n/a
37	chr1:223853949-223853999	HMEC	breast:	n/a
38	chr1:223853949-223853999	NH-A	brain:	n/a
39	chr1:223853949-223853999	PANC-1	pancreas:	n/a
40	chr1:223853928-223853978	HUVEC	blood vessel:	n/a
41	chr1:223853928-223853978	Hela-S3	cervix:	n/a
42	chr1:223853949-223853999	ProgFib	skin:	n/a
43	chr1:223853928-223853978	HCPEpiC	choroid plexus:	n/a
44	chr1:223853949-223853999	SK-N-SH_RA	brain:	n/a
45	chr1:223853928-223853978	HEK293	kidney:	embryo
46	chr1:223853928-223853978	SK-N-MC	brain:	n/a
47	chr1:223853928-223853978	MCF-7	breast:	n/a
48	chr1:223853949-223853999	GM12891	blood:	n/a
49	chr1:223853928-223853978	NHDF-neo	bronchial:	n/a
50	chr1:223853949-223853999	HCM	heart:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:223831956..223833970-chr1:223853050..223855835,2	MCF-7	breast:
2	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:
3	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
4	chr1:223348196..223351831-chr1:223853498..223856683,4	MCF-7	breast:
5	chr1:223853852..223855706-chr1:223946715..223948642,2	K562	blood:

No data

Variant related genes	Relation type
CAPN8	TF binding region
CAPN8	CpG island
ENSG00000227002	Chromatin interaction
ENSG00000203697	Chromatin interaction
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10753427	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915854	1.00[AMR][1000 genomes]
rs10916015	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1222144	1.00[AMR][1000 genomes]
rs1361915	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1539703	1.00[AMR][1000 genomes]
rs1539704	1.00[YRI][hapmap]
rs16842210	1.00[AMR][1000 genomes]
rs16842251	1.00[AMR][1000 genomes]
rs1857549	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1892071	1.00[AMR][1000 genomes]
rs1892074	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1892075	1.00[AMR][1000 genomes]
rs1977898	1.00[AMR][1000 genomes]
rs2000317	1.00[AMR][1000 genomes]
rs2096343	1.00[AMR][1000 genomes]
rs2154115	1.00[AMR][1000 genomes]
rs2186005	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2404288	1.00[AMR][1000 genomes]
rs25655	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370086	1.00[AMR][1000 genomes]
rs28370105	1.00[AMR][1000 genomes]
rs28370108	1.00[AMR][1000 genomes]
rs4653792	1.00[AMR][1000 genomes]
rs4653866	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653869	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6422641	1.00[AMR][1000 genomes]
rs6688648	1.00[AMR][1000 genomes]
rs7538151	1.00[AMR][1000 genomes]
rs7554290	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223851800-223857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:223853000-223854000	Enhancers	Duodenum Mucosa	Duodenum
3	chr1:223853000-223854400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:223853000-223854600	Enhancers	Hela-S3	cervix
5	chr1:223853000-223855800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:223853200-223854000	Enhancers	Fetal Intestine Large	intestine
7	chr1:223853200-223854600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr1:223853400-223854000	Enhancers	Colonic Mucosa	Colon
9	chr1:223853400-223854000	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr1:223853400-223854200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:223853400-223855000	Weak transcription	Gastric	stomach
12	chr1:223853400-223856000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:223853400-223856600	Weak transcription	Lung	lung
14	chr1:223853400-223856800	Enhancers	HMEC	breast
15	chr1:223853400-223857000	Enhancers	Stomach Mucosa	stomach
16	chr1:223853600-223854000	Enhancers	A549	lung
17	chr1:223853800-223854800	Weak transcription	Placenta	Placenta
18	chr1:223853800-223855200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:223853800-223855600	Weak transcription	Pancreas	Pancrea
20	chr1:223853800-223856200	Enhancers	NHEK	skin
21	chr1:223853800-223856600	Weak transcription	Esophagus	oesophagus
22	chr1:223853800-223857000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:223853800-223858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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