Variant report

Variant	rs542213419
Chromosome Location	chr9:71940874-71940875
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	SIN3A	chr9:71939340-71941514	H1-hESC	embryonic stem cell:	n/a	chr9:71939943-71939956 chr9:71940048-71940061
2	MAX	chr9:71940416-71940875	H1-hESC	embryonic stem cell:	n/a	n/a

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	chr9:71937269..71941011-chr9:72000572..72004392,4	MCF-7	breast:
4	chr9:71939857..71941604-chr9:71989524..71992457,2	MCF-7	breast:
5	chr9:71938510..71941284-chr9:71942079..71947019,4	MCF-7	breast:
6	chr9:71939962..71941547-chr9:71947725..71950010,2	MCF-7	breast:
7	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: 9 )
Associated
traits (count: 0)

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:85 , 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	chr9:71939000-71941000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr9:71939000-71941000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr9:71939000-71941200	Active TSS	Ovary	ovary
7	chr9:71939000-71941400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr9:71939000-71942800	Active TSS	Stomach Smooth Muscle	stomach
9	chr9:71939200-71941000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr9:71939200-71941200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr9:71939200-71941400	Active TSS	Left Ventricle	heart
12	chr9:71939200-71944000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:71939400-71941000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr9:71939400-71941000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr9:71939400-71941000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:71939400-71941000	Bivalent/Poised TSS	Fetal Brain Female	brain
17	chr9:71939400-71941000	Active TSS	Hela-S3	cervix
18	chr9:71939400-71941200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:71939400-71941200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:71939400-71941200	Active TSS	Esophagus	oesophagus
21	chr9:71939400-71941200	Active TSS	Lung	lung
22	chr9:71939400-71941400	Active TSS	Colon Smooth Muscle	Colon
23	chr9:71939400-71941400	Active TSS	Psoas Muscle	Psoas
24	chr9:71939400-71941600	Active TSS	Gastric	stomach
25	chr9:71939400-71942200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:71939600-71941000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:71939600-71941000	Active TSS	Pancreas	Pancrea
28	chr9:71939600-71941400	Active TSS	Brain Angular Gyrus	brain
29	chr9:71939600-71942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:71939800-71941000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:71939800-71941000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr9:71939800-71941000	Active TSS	HSMMtube	muscle
33	chr9:71939800-71941200	Active TSS	Rectal Smooth Muscle	rectum
34	chr9:71939800-71941400	Bivalent/Poised TSS	Fetal Stomach	stomach
35	chr9:71939800-71942200	Active TSS	Right Ventricle	heart
36	chr9:71939800-71942600	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr9:71940000-71941800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
38	chr9:71940200-71941000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr9:71940200-71941400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:71940400-71941000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:71940400-71941200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
44	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr9:71940600-71941000	Flanking Bivalent TSS/Enh	Placenta	Placenta
50	chr9:71940600-71941000	Bivalent/Poised TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links