Variant report

Variant	rs11928059
Chromosome Location	chr3:194808181-194808182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:194807913-194808978	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr3:194807523-194808189	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:194808016-194808649	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:194808116-194808318	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr3:194807533-194808207	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr3:194808058-194808596	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF263	chr3:194807678-194808300	HEK293-T-REx	kidney:	n/a	n/a
8	YY1	chr3:194808145-194808967	NT2-D1	testis:	n/a	n/a
9	TCF12	chr3:194807681-194808432	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
XXYLT1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1389726	0.88[EUR][1000 genomes]
rs2642392	0.95[EUR][1000 genomes]
rs2676909	0.95[EUR][1000 genomes]
rs2676911	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2720948	0.92[EUR][1000 genomes]
rs62290284	0.85[EUR][1000 genomes]
rs9823497	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9861985	0.88[EUR][1000 genomes]
rs9883940	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:194797200-194808200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:194801000-194814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:194801200-194808200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:194801200-194814800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:194801200-194814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:194801600-194808400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:194803000-194814400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:194803200-194815800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
12	chr3:194805400-194809200	Enhancers	Fetal Thymus	thymus
13	chr3:194806600-194808200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:194806600-194808200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:194806600-194808800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:194806800-194808400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:194806800-194808400	Enhancers	Thymus	Thymus
18	chr3:194806800-194808800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:194807000-194808400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:194807000-194808400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:194807000-194808800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:194807200-194808200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:194807200-194808400	Enhancers	Pancreas	Pancrea
25	chr3:194807200-194808600	Enhancers	Fetal Heart	heart
26	chr3:194807400-194808200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:194807400-194808600	Enhancers	K562	blood
28	chr3:194807600-194808200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:194807600-194808200	Enhancers	Stomach Mucosa	stomach
30	chr3:194807600-194808800	Enhancers	Esophagus	oesophagus
31	chr3:194807600-194814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:194807800-194808200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr3:194807800-194808400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:194807800-194808400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:194807800-194808400	Enhancers	Adipose Nuclei	Adipose
36	chr3:194807800-194808400	Enhancers	Brain Germinal Matrix	brain
37	chr3:194807800-194808400	Enhancers	Fetal Muscle Trunk	muscle
38	chr3:194807800-194808400	Weak transcription	Lung	lung
39	chr3:194807800-194808400	Enhancers	HepG2	liver
40	chr3:194807800-194808600	Enhancers	Fetal Intestine Large	intestine
41	chr3:194807800-194808800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:194807800-194808800	Enhancers	Fetal Lung	lung
43	chr3:194807800-194808800	Enhancers	Placenta	Placenta
44	chr3:194808000-194808200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:194808000-194808200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr3:194808000-194808200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:194808000-194808200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:194808000-194808200	Genic enhancers	Fetal Intestine Small	intestine
49	chr3:194808000-194808200	Enhancers	Fetal Stomach	stomach
50	chr3:194808000-194808200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links