Variant report

Variant	rs12685109
Chromosome Location	chr9:98169250-98169251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98167871..98172268-chr9:98186784..98190412,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237857	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16905568	1.00[AMR][1000 genomes]
rs16909877	1.00[AMR][1000 genomes]
rs16912126	0.93[ASN][1000 genomes]
rs16912127	0.93[ASN][1000 genomes]
rs16912143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28522014	1.00[AMR][1000 genomes]
rs55758638	1.00[AMR][1000 genomes]
rs55787302	1.00[AMR][1000 genomes]
rs56222079	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1045479	chr9:98115290-98172995	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1051731	chr9:98154815-98201115	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98144000-98172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:98150600-98173600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:98160400-98188400	Weak transcription	Pancreas	Pancrea
4	chr9:98161800-98172200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:98166600-98169400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:98167800-98169600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:98168000-98170000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:98168200-98169800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:98168200-98169800	Enhancers	Fetal Lung	lung
10	chr9:98168200-98170000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:98168400-98169600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:98168400-98169800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:98168400-98169800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:98168400-98170000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:98168400-98170400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr9:98168600-98169800	Enhancers	Brain Germinal Matrix	brain
17	chr9:98168600-98172200	Weak transcription	A549	lung
18	chr9:98168800-98171600	Weak transcription	Hela-S3	cervix
19	chr9:98169000-98169800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:98169000-98172400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:98169200-98169600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:98169200-98171200	Weak transcription	Monocytes-CD14+_RO01746	blood

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