Variant report

Variant	rs12344342
Chromosome Location	chr9:96935458-96935459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:96935277-96935596	K562	blood:	n/a	n/a
2	POLR2A	chr9:96935281-96935654	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:96935408-96935610	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:96935341-96935751	MCF-7	breast:	n/a	n/a
5	POLR2A	chr9:96934947-96935967	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:96935443-96937418	GM12878	blood:	n/a	n/a
7	POLR2A	chr9:96935326-96937156	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:96935438-96935636	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr9:96935395-96935497	A549	lung:	n/a	n/a
10	POLR2A	chr9:96935334-96935694	K562	blood:	n/a	n/a
11	POLR2A	chr9:96935344-96935487	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96902444..96903976-chr9:96934492..96936431,2	K562	blood:
2	chr9:96873193..96875324-chr9:96934781..96937611,2	K562	blood:
3	chr9:96934105..96937234-chr9:96943114..96945589,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269929	TF binding region
MIRLET7F1	TF binding region
MIRLET7A1	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10761319	0.91[EUR][1000 genomes]
rs10761322	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993070	0.90[EUR][1000 genomes]
rs10993087	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7853614	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96929600-96936400	Weak transcription	Gastric	stomach
2	chr9:96929600-96938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:96929800-96936000	Weak transcription	Esophagus	oesophagus
4	chr9:96929800-96944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:96930000-96936200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:96930400-96938200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr9:96930600-96935600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr9:96930600-96935800	Weak transcription	Placenta	Placenta
10	chr9:96930600-96937600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:96930600-96943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:96930600-96943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:96931000-96936000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr9:96931000-96937200	Enhancers	Fetal Heart	heart
15	chr9:96931200-96935600	Enhancers	Liver	Liver
16	chr9:96931200-96935600	Weak transcription	Stomach Mucosa	stomach
17	chr9:96931200-96936000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:96931200-96936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:96931200-96936400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:96931200-96938200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr9:96931200-96938800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:96931400-96935800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:96931800-96935800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:96931800-96936000	Enhancers	Adipose Nuclei	Adipose
26	chr9:96931800-96936000	Weak transcription	Thymus	Thymus
27	chr9:96931800-96939000	Weak transcription	Fetal Brain Male	brain
28	chr9:96932000-96936400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:96932000-96938200	Enhancers	Brain Anterior Caudate	brain
30	chr9:96932200-96935600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:96932200-96935800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:96932200-96936000	Weak transcription	HSMMtube	muscle
33	chr9:96932400-96935600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr9:96932400-96935600	Weak transcription	Brain Germinal Matrix	brain
35	chr9:96932400-96936000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:96932400-96938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:96932600-96935800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:96932600-96936400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:96932800-96937800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr9:96933400-96935600	Enhancers	Primary B cells from peripheral blood	blood
41	chr9:96933400-96935600	Weak transcription	Fetal Kidney	kidney
42	chr9:96933400-96935600	Genic enhancers	Fetal Stomach	stomach
43	chr9:96933400-96936000	Weak transcription	Fetal Lung	lung
44	chr9:96933400-96936800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:96933400-96937000	Enhancers	Right Atrium	heart
46	chr9:96933400-96939000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:96933600-96935600	Weak transcription	HMEC	breast
48	chr9:96933600-96936000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:96933600-96939400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:96933600-96939800	Strong transcription	Hela-S3	cervix

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