Variant report

Variant	rs3729496
Chromosome Location	chr10:50821191-50821192
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr10:50821165-50821429	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr10:50820585-50821686	HEK293-T-REx	kidney:	n/a	n/a
3	SIN3A	chr10:50820906-50821449	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr10:50818492-50822122	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:50820978-50821357	SK-N-MC	brain:	n/a	n/a
6	CTBP2	chr10:50819126-50822240	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr10:50820904-50821231	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr10:50820823-50821194	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr10:50820979-50821289	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:50821161-50821211	SKMC	muscle:	n/a
2	chr10:50821161-50821211	ProgFib	skin:	n/a
3	chr10:50821161-50821211	AG04449	skin:	fetal
4	chr10:50821161-50821211	AG09309	skin:	n/a
5	chr10:50821161-50821211	HEK293	kidney:	embryo
6	chr10:50821161-50821211	MCF-7	breast:	n/a
7	chr10:50821161-50821211	HRCEpiC	kidney:	n/a
8	chr10:50821161-50821211	LNCaP	prostate:	n/a
9	chr10:50821161-50821211	AG09319	gingival:	n/a
10	chr10:50821161-50821211	HCF	heart:	n/a
11	chr10:50821161-50821211	SK-N-SH_RA	brain:	n/a
12	chr10:50821161-50821211	A549	lung:	n/a
13	chr10:50821161-50821211	HCM	heart:	n/a
14	chr10:50821161-50821211	HCT-116	colon:	n/a
15	chr10:50821161-50821211	GM12891	blood:	n/a
16	chr10:50821161-50821211	HL-60	blood:	n/a
17	chr10:50821161-50821211	HIPEpiC	eye:	n/a
18	chr10:50821161-50821211	U87	brain:	n/a
19	chr10:50821161-50821211	BE2_C	brain:	n/a
20	chr10:50821161-50821211	NB4	blood:	n/a
21	chr10:50821161-50821211	CMK	blood:	n/a
22	chr10:50821161-50821211	GM06990	blood:	n/a
23	chr10:50821161-50821211	NH-A	brain:	n/a
24	chr10:50821161-50821211	Hela-S3	cervix:	n/a
25	chr10:50821161-50821211	SK-N-SH	brain:	n/a
26	chr10:50821161-50821211	PANC-1	pancreas:	n/a
27	chr10:50821161-50821211	HAEpiC	amniotic membrane:	n/a
28	chr10:50821161-50821211	MCF10A-Er-Src	breast:	n/a
29	chr10:50821161-50821211	AG10803	skin:	n/a
30	chr10:50821161-50821211	HRE	kidney:	n/a
31	chr10:50821161-50821211	ECC-1	luminal epithelium:	n/a
32	chr10:50821161-50821211	PrEC	prostate:	n/a
33	chr10:50821161-50821211	GM12892	blood:	n/a
34	chr10:50821161-50821211	HRPEpiC	eye:	n/a
35	chr10:50821161-50821211	NHBE	bronchial:	n/a
36	chr10:50821161-50821211	AG04450	lung:	fetal
37	chr10:50821161-50821211	Caco-2	colon:	n/a
38	chr10:50821161-50821211	GM12878	blood:	n/a
39	chr10:50821161-50821211	HMEC	breast:	n/a
40	chr10:50821161-50821211	HUVEC	blood vessel:	n/a
41	chr10:50821161-50821211	SAEC	small airway:	n/a
42	chr10:50821161-50821211	K562	blood:	n/a
43	chr10:50821161-50821211	Jurkat	blood:	n/a
44	chr10:50821161-50821211	RPTEC	kidney:	n/a
45	chr10:50821161-50821211	HNPCEpiC	eye:	n/a
46	chr10:50821161-50821211	HEEpiC	esophagus:	n/a
47	chr10:50821161-50821211	NT2-D1	testis:	n/a
48	chr10:50821161-50821211	T-47D	breast:	n/a
49	chr10:50821161-50821211	HPAEpiC	pulmonary alveolar:	n/a
50	chr10:50821161-50821211	ovcar-3	ovarian:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC18A3-1	chr10:50821165-50821248	NONHSAT013316

No data

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10857518	0.91[JPT][hapmap]
rs3810947	0.95[JPT][hapmap]
rs7903315	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv1037405	chr10:50800817-50940545	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv895378	chr10:50801342-50955649	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv550819	chr10:50815512-50835264	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3518245	chr10:50817146-50821244	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3518246	chr10:50817146-50821244	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50817800-50822200	Enhancers	Pancreas	Pancrea
2	chr10:50818400-50821200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr10:50818400-50822400	Bivalent Enhancer	Fetal Brain Male	brain
4	chr10:50818800-50821400	Bivalent Enhancer	Fetal Intestine Small	intestine
5	chr10:50819200-50821200	Bivalent Enhancer	Placenta	Placenta
6	chr10:50819200-50821400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:50819200-50821800	Bivalent Enhancer	Brain Hippocampus Middle	brain
8	chr10:50819400-50821600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
9	chr10:50819400-50821800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:50819400-50823000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
11	chr10:50819600-50821400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr10:50819600-50821400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:50819600-50822200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr10:50819800-50821200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr10:50820000-50821800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:50820200-50821200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr10:50820200-50821200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr10:50820200-50822000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:50820200-50822400	Weak transcription	Right Atrium	heart
20	chr10:50820800-50821200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr10:50820800-50821400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr10:50820800-50821600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:50820800-50821800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr10:50820800-50821800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:50820800-50822000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr10:50821000-50821200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr10:50821000-50821200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr10:50821000-50821200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
29	chr10:50821000-50821200	Bivalent Enhancer	Lung	lung
30	chr10:50821000-50821800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:50821000-50821800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr10:50821000-50821800	Bivalent Enhancer	HMEC	breast
33	chr10:50821000-50822200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:50821000-50822400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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