Variant report

Variant	rs12342783
Chromosome Location	chr9:71941071-71941072
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	ZKSCAN1	chr9:71940959-71941199	Hela-S3	cervix:	n/a	n/a
2	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]
rs12342833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60600407	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61041964	0.89[AFR][1000 genomes];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:76 , 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	chr9:71939000-71941200	Active TSS	Ovary	ovary
5	chr9:71939000-71941400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr9:71939000-71942800	Active TSS	Stomach Smooth Muscle	stomach
7	chr9:71939200-71941200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:71939200-71941400	Active TSS	Left Ventricle	heart
9	chr9:71939200-71944000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr9:71939400-71941200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:71939400-71941200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:71939400-71941200	Active TSS	Esophagus	oesophagus
13	chr9:71939400-71941200	Active TSS	Lung	lung
14	chr9:71939400-71941400	Active TSS	Colon Smooth Muscle	Colon
15	chr9:71939400-71941400	Active TSS	Psoas Muscle	Psoas
16	chr9:71939400-71941600	Active TSS	Gastric	stomach
17	chr9:71939400-71942200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:71939600-71941400	Active TSS	Brain Angular Gyrus	brain
19	chr9:71939600-71942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:71939800-71941200	Active TSS	Rectal Smooth Muscle	rectum
21	chr9:71939800-71941400	Bivalent/Poised TSS	Fetal Stomach	stomach
22	chr9:71939800-71942200	Active TSS	Right Ventricle	heart
23	chr9:71939800-71942600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr9:71940000-71941800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
25	chr9:71940200-71941400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:71940400-71941200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:71940600-71941200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
28	chr9:71940600-71941200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
29	chr9:71940600-71941200	Bivalent Enhancer	Fetal Brain Male	brain
30	chr9:71940600-71941200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
31	chr9:71940600-71941200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
32	chr9:71940600-71941400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr9:71940600-71941400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
34	chr9:71940600-71941400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr9:71940600-71941400	Bivalent/Poised TSS	Fetal Thymus	thymus
36	chr9:71940800-71941200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:71940800-71941200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:71940800-71941200	Bivalent Enhancer	Fetal Kidney	kidney
39	chr9:71940800-71941200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr9:71940800-71941200	Bivalent Enhancer	HepG2	liver
41	chr9:71940800-71941400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:71940800-71941400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr9:71940800-71941400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr9:71940800-71941400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:71940800-71941400	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr9:71940800-71941400	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
47	chr9:71940800-71941400	Flanking Active TSS	HMEC	breast
48	chr9:71940800-71941600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
49	chr9:71941000-71941200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:71941000-71941200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links