Variant report

Variant	rs28616242
Chromosome Location	chr9:136994633-136994634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136924138..136926456-chr9:136992435..136994795,2	MCF-7	breast:
2	chr9:136992413..136997235-chr9:136998349..137003411,7	K562	blood:
3	chr9:136994448..136996074-chr9:136999589..137002197,2	K562	blood:

Variant related genes	Relation type
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28408860	0.96[ASN][1000 genomes]
rs28437234	0.96[ASN][1000 genomes]
rs28473627	0.96[ASN][1000 genomes]
rs28580780	0.96[ASN][1000 genomes]
rs28581991	0.84[ASN][1000 genomes]
rs28587783	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28602914	0.91[ASN][1000 genomes]
rs28759362	0.94[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	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136990000-136994800	Weak transcription	Hela-S3	cervix
2	chr9:136990800-136996200	Enhancers	Fetal Muscle Leg	muscle
3	chr9:136991000-136999400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:136991200-136996000	Weak transcription	Pancreas	Pancrea
5	chr9:136992800-136996600	Enhancers	Fetal Muscle Trunk	muscle
6	chr9:136993600-136995400	Enhancers	HSMMtube	muscle
7	chr9:136994000-136995200	Enhancers	Esophagus	oesophagus
8	chr9:136994000-136995400	Enhancers	Placenta	Placenta
9	chr9:136994000-136995400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr9:136994000-136995400	Enhancers	HSMM	muscle
11	chr9:136994200-136994800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr9:136994200-136995000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:136994200-136995000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:136994200-136995200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:136994200-136995200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr9:136994200-136995400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:136994400-136995000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:136994400-136995000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr9:136994400-136995400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:136994400-136995800	Enhancers	HepG2	liver
21	chr9:136994400-136996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:136994400-136996000	Enhancers	Stomach Smooth Muscle	stomach
23	chr9:136994400-136996200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:136994400-136996400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:136994400-136999400	Weak transcription	Primary B cells from cord blood	blood
26	chr9:136994600-136994800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:136994600-136994800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:136994600-136995200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:136994600-136999200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:136994600-136999400	Weak transcription	Spleen	Spleen
31	chr9:136994600-136999800	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links