Variant report

Variant	rs3731249
Chromosome Location	chr9:21970916-21970917
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	SP1	chr9:21970709-21971117	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:21968130-21971125	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:21970891-21971122	ECC-1	luminal epithelium:	n/a	n/a
4	CTBP2	chr9:21969213-21971396	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:21964929-21971504	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr9:21970906-21971158	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr9:21970206-21971225	SK-N-MC	brain:	n/a	n/a
8	CHD2	chr9:21970848-21971129	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr9:21970820-21970970	GM12871	blood:	n/a	n/a
10	BACH1	chr9:21970767-21971051	H1-hESC	embryonic stem cell:	n/a	n/a
11	SUZ12	chr9:21969851-21971369	H1-hESC	embryonic stem cell:	n/a	n/a
12	SUZ12	chr9:21964929-21971601	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
CDKN2A	TF binding region

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10965249	1.00[CHB][hapmap]
rs10965251	1.00[CHB][hapmap]
rs10965252	1.00[CHB][hapmap]
rs10965253	1.00[CHB][hapmap]
rs36228834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36229158	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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21965400-21972000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:21966200-21971000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:21966200-21972000	Strong transcription	Dnd41	blood
4	chr9:21967200-21971200	ZNF genes & repeats	HMEC	breast
5	chr9:21968200-21971400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr9:21968400-21971200	ZNF genes & repeats	HSMM	muscle
7	chr9:21968800-21971000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr9:21968800-21971200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:21969000-21971600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr9:21970000-21971000	ZNF genes & repeats	GM12878-XiMat	blood
11	chr9:21970000-21971200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:21970200-21971400	ZNF genes & repeats	Lung	lung
13	chr9:21970200-21971400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr9:21970400-21971000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:21970400-21971000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:21970400-21971000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr9:21970400-21971400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr9:21970400-21971400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr9:21970600-21971000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
20	chr9:21970600-21971000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:21970600-21971200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr9:21970600-21971200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:21970600-21971200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:21970600-21971200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
25	chr9:21970600-21971400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr9:21970600-21971400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:21970600-21971400	Bivalent Enhancer	HUVEC	blood vessel
28	chr9:21970600-21971600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr9:21970800-21971000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:21970800-21971000	Bivalent Enhancer	Brain Substantia Nigra	brain
31	chr9:21970800-21971000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
32	chr9:21970800-21971000	Flanking Bivalent TSS/Enh	Spleen	Spleen
33	chr9:21970800-21971200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
34	chr9:21970800-21971200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr9:21970800-21971200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:21970800-21971200	Bivalent Enhancer	Fetal Brain Male	brain
37	chr9:21970800-21971200	Bivalent Enhancer	Gastric	stomach
38	chr9:21970800-21971200	Bivalent Enhancer	Right Ventricle	heart
39	chr9:21970800-21971400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr9:21970800-21971400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:21970800-21971600	Bivalent Enhancer	Fetal Heart	heart
42	chr9:21970800-21971800	Strong transcription	Hela-S3	cervix
43	chr9:21970800-21972200	Weak transcription	HSMMtube	muscle

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