Variant report

Variant	rs12342833
Chromosome Location	chr9:71941258-71941259
allele	G/T
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	SIN3A	chr9:71939340-71941514	H1-hESC	embryonic stem cell:	n/a	chr9:71939943-71939956 chr9:71940048-71940061

No.	Distal block	Cell Line	Cell type
1	chr9:71939667..71941572-chr9:71995013..71999921,5	MCF-7	breast:
2	chr9:71810860..71813115-chr9:71939521..71941834,2	MCF-7	breast:
3	chr9:71939857..71941604-chr9:71989524..71992457,2	MCF-7	breast:
4	chr9:71938510..71941284-chr9:71942079..71947019,4	MCF-7	breast:
5	chr9:71939962..71941547-chr9:71947725..71950010,2	MCF-7	breast:
6	chr9:71940098..71942516-chr9:71992469..71994657,3	MCF-7	breast:

Variant related genes	Relation type
FAM189A2	TF binding region
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11788088	0.88[EUR][1000 genomes]
rs11789518	0.88[EUR][1000 genomes]
rs11790372	0.88[EUR][1000 genomes]
rs11793624	0.80[EUR][1000 genomes]
rs11795221	0.88[EUR][1000 genomes]
rs12342783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60600407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61041964	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3374800	chr9:71939157-71942005	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3417138	chr9:71939382-71941480	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71937600-71942800	Active TSS	Fetal Heart	heart
2	chr9:71938800-71941400	Active TSS	Brain Anterior Caudate	brain
3	chr9:71938800-71942800	Active TSS	Right Atrium	heart
4	chr9:71939000-71941400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:71939000-71942800	Active TSS	Stomach Smooth Muscle	stomach
6	chr9:71939200-71941400	Active TSS	Left Ventricle	heart
7	chr9:71939200-71944000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr9:71939400-71941400	Active TSS	Colon Smooth Muscle	Colon
9	chr9:71939400-71941400	Active TSS	Psoas Muscle	Psoas
10	chr9:71939400-71941600	Active TSS	Gastric	stomach
11	chr9:71939400-71942200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:71939600-71941400	Active TSS	Brain Angular Gyrus	brain
13	chr9:71939600-71942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:71939800-71941400	Bivalent/Poised TSS	Fetal Stomach	stomach
15	chr9:71939800-71942200	Active TSS	Right Ventricle	heart
16	chr9:71939800-71942600	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr9:71940000-71941800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
18	chr9:71940200-71941400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:71940600-71941400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr9:71940600-71941400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr9:71940600-71941400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr9:71940600-71941400	Bivalent/Poised TSS	Fetal Thymus	thymus
23	chr9:71940800-71941400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:71940800-71941400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
25	chr9:71940800-71941400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr9:71940800-71941400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:71940800-71941400	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr9:71940800-71941400	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
29	chr9:71940800-71941400	Flanking Active TSS	HMEC	breast
30	chr9:71940800-71941600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
31	chr9:71941000-71941400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
32	chr9:71941000-71941400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr9:71941000-71941400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
34	chr9:71941000-71941400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr9:71941000-71941400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr9:71941000-71941400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:71941000-71941400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
38	chr9:71941000-71941400	Flanking Bivalent TSS/Enh	Hela-S3	cervix
39	chr9:71941000-71941600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:71941000-71941600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:71941000-71941600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr9:71941000-71941600	Enhancers	Pancreas	Pancrea
43	chr9:71941000-71941600	Bivalent Enhancer	NHEK	skin
44	chr9:71941000-71941800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:71941000-71942400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
46	chr9:71941000-71946800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr9:71941200-71941400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:71941200-71941400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:71941200-71941400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
50	chr9:71941200-71941400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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