Variant report

Variant	rs540662372
Chromosome Location	chr12:31079046-31079047
allele	C/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	MXI1	chr12:31078809-31079564	H1-hESC	embryonic stem cell:	n/a	chr12:31079353-31079368
2	CTBP2	chr12:31078500-31079604	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr12:31078898-31079751	H1-hESC	embryonic stem cell:	n/a	chr12:31079579-31079592 chr12:31079650-31079661 chr12:31079280-31079291 chr12:31079518-31079529 chr12:31079368-31079379
4	ZNF263	chr12:31078575-31079189	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr12:31078945-31080180	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr12:31078930-31080600	H1-neurons	neurons:	n/a	chr12:31079230-31079243 chr12:31080511-31080524 chr12:31079478-31079496 chr12:31079273-31079283 chr12:31079636-31079649 chr12:31080050-31080063
7	TCF12	chr12:31078891-31079222	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:31078957-31079635	H1-neurons	neurons:	n/a	n/a
9	MXI1	chr12:31078649-31082379	SK-N-SH	brain:	n/a	chr12:31081271-31081286 chr12:31079353-31079368
10	MYC	chr12:31078979-31079572	H1-hESC	embryonic stem cell:	n/a	chr12:31079154-31079164
11	POLR2A	chr12:31078506-31080634	SK-N-MC	brain:	n/a	n/a
12	CHD2	chr12:31078905-31079452	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
TSPAN11	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1052957	chr12:30951520-31191197	Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv541439	chr12:30951520-31191197	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1052869	chr12:30951520-31399162	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv2422447	chr12:30954811-31449815	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv832362	chr12:30957786-31124983	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1053711	chr12:30959987-31156297	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv558030	chr12:30969675-31266287	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
10	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv1051648	chr12:31069125-31103671	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2422366	chr12:31071959-31276836	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv658	chr12:31072400-31108649	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3431172	chr12:31078685-31080783	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31078400-31079200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
2	chr12:31078400-31080000	Enhancers	Fetal Heart	heart
3	chr12:31078600-31079200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:31078600-31079200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
5	chr12:31078600-31079200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr12:31078600-31079200	Enhancers	Left Ventricle	heart
7	chr12:31078600-31079200	Enhancers	Lung	lung
8	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
9	chr12:31078800-31079200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:31078800-31079200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:31078800-31079200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:31078800-31079200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
17	chr12:31078800-31079200	Flanking Active TSS	Fetal Brain Female	brain
18	chr12:31078800-31079200	Enhancers	Pancreas	Pancrea
19	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
20	chr12:31078800-31079200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
21	chr12:31078800-31079400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr12:31078800-31079400	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr12:31078800-31079400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
24	chr12:31078800-31080000	Active TSS	Fetal Kidney	kidney
25	chr12:31078800-31080600	Enhancers	Spleen	Spleen
26	chr12:31079000-31079200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:31079000-31079200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:31079000-31079200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
30	chr12:31079000-31079200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr12:31079000-31079200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:31079000-31079200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr12:31079000-31079200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
35	chr12:31079000-31079200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:31079000-31079200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
39	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr12:31079000-31079200	Bivalent Enhancer	Fetal Lung	lung
41	chr12:31079000-31079200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
42	chr12:31079000-31079200	Flanking Active TSS	Right Atrium	heart
43	chr12:31079000-31079200	Flanking Active TSS	Right Ventricle	heart
44	chr12:31079000-31079200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
45	chr12:31079000-31079200	Bivalent Enhancer	HepG2	liver
46	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	NH-A	brain
47	chr12:31079000-31079200	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
48	chr12:31079000-31079400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:31079000-31079400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr12:31079000-31079400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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