Variant report

Variant	rs58976742
Chromosome Location	chr9:71941488-71941489
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	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	chr9:71941355..71943004-chr9:71944003..71945586,2	MCF-7	breast:
3	chr9:71810860..71813115-chr9:71939521..71941834,2	MCF-7	breast:
4	chr9:71939857..71941604-chr9:71989524..71992457,2	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: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs72713170	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713176	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73649647	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73649649	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73649650	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73649651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71937600-71942800	Active TSS	Fetal Heart	heart
2	chr9:71938800-71942800	Active TSS	Right Atrium	heart
3	chr9:71939000-71942800	Active TSS	Stomach Smooth Muscle	stomach
4	chr9:71939200-71944000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr9:71939400-71941600	Active TSS	Gastric	stomach
6	chr9:71939400-71942200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:71939600-71942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:71939800-71942200	Active TSS	Right Ventricle	heart
9	chr9:71939800-71942600	Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr9:71940000-71941800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
11	chr9:71940800-71941600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr9:71941000-71941600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:71941000-71941600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:71941000-71941600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr9:71941000-71941600	Enhancers	Pancreas	Pancrea
16	chr9:71941000-71941600	Bivalent Enhancer	NHEK	skin
17	chr9:71941000-71941800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:71941000-71942400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
19	chr9:71941000-71946800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:71941200-71941600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:71941200-71941800	Flanking Active TSS	Ovary	ovary
22	chr9:71941200-71942200	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr9:71941400-71941600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr9:71941400-71941600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr9:71941400-71941600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:71941400-71941600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:71941400-71941600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:71941400-71941600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr9:71941400-71941600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:71941400-71941600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:71941400-71941600	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr9:71941400-71941600	Flanking Active TSS	Left Ventricle	heart
33	chr9:71941400-71941600	Active TSS	Lung	lung
34	chr9:71941400-71941600	Enhancers	Psoas Muscle	Psoas
35	chr9:71941400-71941600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr9:71941400-71941600	Bivalent/Poised TSS	Hela-S3	cervix
37	chr9:71941400-71941600	Enhancers	HMEC	breast
38	chr9:71941400-71941800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:71941400-71942200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:71941400-71942400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr9:71941400-71946600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:71941400-71946600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:71941400-71954400	Weak transcription	Brain Anterior Caudate	brain

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