Variant report

Variant	rs12685485
Chromosome Location	chr9:97411580-97411581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97399795..97401859-chr9:97411374..97414324,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165140	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12684841	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16910850	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16910853	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16910860	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296707	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28369691	0.82[EUR][1000 genomes]
rs28402377	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402378	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402384	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402386	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402389	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402390	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402396	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402397	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402401	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402404	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4111369	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59327242	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7019207	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7028990	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7035325	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73523269	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73523271	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7849320	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850385	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7859022	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859489	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97402400-97420000	Weak transcription	Right Atrium	heart
2	chr9:97402600-97415400	Weak transcription	Spleen	Spleen
3	chr9:97402800-97411600	Weak transcription	Primary B cells from cord blood	blood
4	chr9:97405800-97418400	Weak transcription	Fetal Stomach	stomach
5	chr9:97407000-97411600	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:97407000-97411800	Weak transcription	Placenta	Placenta
7	chr9:97408800-97411600	Weak transcription	Fetal Intestine Small	intestine
8	chr9:97409600-97411600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:97410000-97418000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr9:97410200-97413600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:97410200-97413600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:97410200-97413600	Enhancers	Stomach Mucosa	stomach
13	chr9:97410200-97413800	Enhancers	HMEC	breast
14	chr9:97410400-97411600	Weak transcription	Small Intestine	intestine
15	chr9:97410400-97411600	Enhancers	NHEK	skin
16	chr9:97410400-97412000	Enhancers	Esophagus	oesophagus
17	chr9:97410400-97413600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:97410400-97413600	Enhancers	Duodenum Mucosa	Duodenum
19	chr9:97410600-97412200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr9:97410800-97412200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:97410800-97412200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr9:97410800-97412200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr9:97410800-97412200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:97410800-97412200	Enhancers	HSMM	muscle
25	chr9:97410800-97412200	Enhancers	NH-A	brain
26	chr9:97410800-97412400	Enhancers	Primary hematopoietic stem cells	blood
27	chr9:97410800-97412400	Enhancers	A549	lung
28	chr9:97410800-97413600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:97411000-97411800	Enhancers	Gastric	stomach
30	chr9:97411000-97412200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:97411000-97412200	Enhancers	HSMMtube	muscle
32	chr9:97411000-97412200	Enhancers	Osteobl	bone
33	chr9:97411000-97416200	Weak transcription	Lung	lung
34	chr9:97411000-97417800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:97411200-97411600	Enhancers	Hela-S3	cervix
36	chr9:97411200-97411800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:97411200-97412000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:97411400-97411800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:97411400-97412000	Enhancers	Colon Smooth Muscle	Colon

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