Variant report

Variant	rs11817206
Chromosome Location	chr10:52395375-52395376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:52394923-52395575	U87	brain:	n/a	n/a
2	FOS	chr10:52395124-52395384	MCF10A-Er-Src	breast:	n/a	chr10:52395198-52395207
3	NFIC	chr10:52394935-52395454	SK-N-SH	brain:	n/a	n/a
4	JUND	chr10:52395111-52395486	SK-N-SH	brain:	n/a	chr10:52395198-52395207
5	POLR2A	chr10:52394962-52395444	U87	brain:	n/a	n/a
6	NFIC	chr10:52395048-52395554	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr10:52394959-52395444	U87	brain:	n/a	n/a
8	FOS	chr10:52395126-52395412	MCF10A-Er-Src	breast:	n/a	chr10:52395198-52395207
9	PBX3	chr10:52395056-52395425	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr10:52394946-52395511	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:52395375-52395425	AoSMC	blood vessel:	n/a
2	chr10:52395375-52395425	K562	blood:	n/a
3	chr10:52395375-52395425	ECC-1	luminal epithelium:	n/a
4	chr10:52395375-52395425	A549	lung:	n/a
5	chr10:52395375-52395425	NB4	blood:	n/a
6	chr10:52395375-52395425	HIPEpiC	eye:	n/a
7	chr10:52395375-52395425	Hela-S3	cervix:	n/a
8	chr10:52395375-52395425	GM19239	blood:	n/a
9	chr10:52395375-52395425	Caco-2	colon:	n/a
10	chr10:52395375-52395425	PFSK-1	brain:	n/a
11	chr10:52395375-52395425	SK-N-SH	brain:	n/a
12	chr10:52395375-52395425	SK-N-SH_RA	brain:	n/a
13	chr10:52395375-52395425	T-47D	breast:	n/a
14	chr10:52395375-52395425	ProgFib	skin:	n/a
15	chr10:52395375-52395425	HCM	heart:	n/a
16	chr10:52395375-52395425	HEK293	kidney:	embryo
17	chr10:52395375-52395425	RPTEC	kidney:	n/a
18	chr10:52395375-52395425	NHBE	bronchial:	n/a
19	chr10:52395375-52395425	GM12891	blood:	n/a
20	chr10:52395375-52395425	AG09319	gingival:	n/a
21	chr10:52395375-52395425	AG04449	skin:	fetal
22	chr10:52395375-52395425	MCF10A-Er-Src	breast:	n/a
23	chr10:52395375-52395425	IMR90	lung:	fetal
24	chr10:52395375-52395425	BE2_C	brain:	n/a
25	chr10:52395375-52395425	HCPEpiC	choroid plexus:	n/a
26	chr10:52395375-52395425	CMK	blood:	n/a
27	chr10:52395375-52395425	GM06990	blood:	n/a
28	chr10:52395375-52395425	GM12878	blood:	n/a
29	chr10:52395375-52395425	AG04450	lung:	fetal
30	chr10:52395375-52395425	GM12892	blood:	n/a
31	chr10:52395375-52395425	SAEC	small airway:	n/a
32	chr10:52395375-52395425	NHDF-neo	bronchial:	n/a
33	chr10:52395375-52395425	HPAEpiC	pulmonary alveolar:	n/a
34	chr10:52395375-52395425	PANC-1	pancreas:	n/a
35	chr10:52395375-52395425	BJ	skin:	n/a
36	chr10:52395375-52395425	NT2-D1	testis:	n/a
37	chr10:52395375-52395425	HL-60	blood:	n/a
38	chr10:52395375-52395425	HMEC	breast:	n/a
39	chr10:52395375-52395425	SK-N-MC	brain:	n/a
40	chr10:52395375-52395425	PrEC	prostate:	n/a
41	chr10:52395375-52395425	HUVEC	blood vessel:	n/a
42	chr10:52395375-52395425	Jurkat	blood:	n/a
43	chr10:52395375-52395425	Hepatocyte	liver:	n/a
44	chr10:52395375-52395425	HAEpiC	amniotic membrane:	n/a
45	chr10:52395375-52395425	HCF	heart:	n/a
46	chr10:52395375-52395425	HNPCEpiC	eye:	n/a
47	chr10:52395375-52395425	HRE	kidney:	n/a
48	chr10:52395375-52395425	LNCaP	prostate:	n/a
49	chr10:52395375-52395425	SKMC	muscle:	n/a
50	chr10:52395375-52395425	ovcar-3	ovarian:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52154324..52156059-chr10:52394056..52396919,2	K562	blood:
2	chr10:52389046..52395992-chr10:52408718..52416095,10	K562	blood:
3	chr10:52394806..52396341-chr10:52398491..52401368,2	K562	blood:
4	chr10:52394806..52397022-chr10:52398491..52400637,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASAH2B-2	chr10:52389337-52401211	ENSG00000226200.2

No data

Variant related genes	Relation type
ENSG00000231588	TF binding region
ENSG00000231588	CpG island
ENSG00000231345	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11005981	1.00[AMR][1000 genomes]
rs11812196	1.00[AMR][1000 genomes]
rs11812413	1.00[AMR][1000 genomes]
rs11812958	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11813457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11816013	1.00[AMR][1000 genomes]
rs11816953	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12243876	1.00[AMR][1000 genomes]
rs12259376	1.00[AMR][1000 genomes]
rs12267585	1.00[AMR][1000 genomes]
rs12267811	1.00[AMR][1000 genomes]
rs7898659	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7908477	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52385800-52396000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52385800-52396800	Weak transcription	Fetal Brain Male	brain
3	chr10:52385800-52397000	Weak transcription	Psoas Muscle	Psoas
4	chr10:52385800-52397000	Weak transcription	Small Intestine	intestine
5	chr10:52386000-52395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:52386000-52396000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:52386000-52397000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr10:52386000-52400400	Weak transcription	Fetal Lung	lung
9	chr10:52386200-52396200	Weak transcription	Primary B cells from cord blood	blood
10	chr10:52386200-52396200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:52389600-52396000	Weak transcription	GM12878-XiMat	blood
12	chr10:52390200-52397000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:52390200-52397000	Weak transcription	Brain Hippocampus Middle	brain
14	chr10:52390800-52396600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:52393600-52395400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:52394000-52395400	Weak transcription	Primary T cells from cord blood	blood
17	chr10:52394600-52395600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:52394600-52396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr10:52394600-52397000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:52394600-52397000	Enhancers	Osteobl	bone
21	chr10:52394600-52397200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr10:52394600-52397400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:52394800-52395400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:52394800-52395400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:52394800-52395400	Enhancers	NHDF-Ad	bronchial
26	chr10:52394800-52395600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:52394800-52395800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:52394800-52395800	Enhancers	HMEC	breast
29	chr10:52394800-52395800	Enhancers	HSMM	muscle
30	chr10:52394800-52396400	Enhancers	NHLF	lung
31	chr10:52394800-52396600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:52394800-52397200	Enhancers	NH-A	brain
33	chr10:52394800-52397400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:52395000-52395400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr10:52395000-52396000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:52395000-52396000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr10:52395000-52396200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr10:52395000-52396200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr10:52395000-52396200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr10:52395000-52396200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr10:52395000-52396600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:52395200-52395400	Enhancers	Esophagus	oesophagus
43	chr10:52395200-52395400	Bivalent Enhancer	HUVEC	blood vessel
44	chr10:52395200-52395800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:52395200-52396200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:52395200-52396200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr10:52395200-52396200	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links