Variant report

Variant	rs12002458
Chromosome Location	chr9:96032279-96032280
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95963970..95967338-chr9:96031466..96034520,4	MCF-7	breast:
2	chr9:95894565..95896559-chr9:96029848..96032324,3	MCF-7	breast:
3	chr9:96031002..96033889-chr9:96054766..96056990,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131669	Chromatin interaction
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10992646	1.00[ASN][1000 genomes]
rs10992647	1.00[ASN][1000 genomes]
rs10992649	1.00[ASN][1000 genomes]
rs10992650	1.00[ASN][1000 genomes]
rs10992651	1.00[ASN][1000 genomes]
rs10992654	1.00[ASN][1000 genomes]
rs10992656	1.00[ASN][1000 genomes]
rs10992657	1.00[ASN][1000 genomes]
rs10992661	1.00[ASN][1000 genomes]
rs10992681	0.82[AMR][1000 genomes]
rs10992699	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107614	0.83[AMR][1000 genomes]
rs1107615	0.83[AMR][1000 genomes]
rs11787888	0.87[AMR][1000 genomes]
rs11789723	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11793893	0.83[AMR][1000 genomes]
rs12000967	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001073	0.83[AMR][1000 genomes]
rs12005950	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006039	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552158	1.00[ASN][1000 genomes]
rs13283550	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287544	0.83[AMR][1000 genomes]
rs13289160	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290796	0.83[AMR][1000 genomes]
rs13301530	0.83[AMR][1000 genomes]
rs1931364	1.00[ASN][1000 genomes]
rs34085543	0.87[AMR][1000 genomes]
rs34834050	0.87[AMR][1000 genomes]
rs35199621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35438673	0.80[AMR][1000 genomes]
rs35566702	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081907	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744213	1.00[ASN][1000 genomes]
rs55981123	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479471	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479474	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022051	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7023262	1.00[ASN][1000 genomes]
rs7042943	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848843	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855391	0.83[AMR][1000 genomes]
rs7857220	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866300	1.00[ASN][1000 genomes]
rs7867954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873162	0.83[AMR][1000 genomes]
rs7874101	0.80[AMR][1000 genomes]
rs7875384	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:96011200-96032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:96011200-96033400	Weak transcription	A549	lung
5	chr9:96012800-96032600	Weak transcription	Fetal Brain Male	brain
6	chr9:96014000-96033800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr9:96014400-96032800	Strong transcription	Fetal Brain Female	brain
8	chr9:96017400-96033200	Weak transcription	Brain Substantia Nigra	brain
9	chr9:96018400-96033200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:96024200-96033600	Strong transcription	Fetal Stomach	stomach
11	chr9:96025400-96035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:96025600-96041200	Weak transcription	Psoas Muscle	Psoas
13	chr9:96026200-96033200	Strong transcription	Brain Germinal Matrix	brain
14	chr9:96027000-96036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:96027200-96035200	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:96027200-96051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:96027600-96032800	Weak transcription	Placenta	Placenta
20	chr9:96028600-96033000	Weak transcription	Small Intestine	intestine
21	chr9:96028600-96036200	Weak transcription	Fetal Heart	heart
22	chr9:96029200-96033600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:96029200-96033600	Enhancers	Dnd41	blood
24	chr9:96029200-96033800	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:96029800-96032600	Strong transcription	Brain Cingulate Gyrus	brain
26	chr9:96029800-96033400	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr9:96029800-96033600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:96030000-96033000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:96030000-96033600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:96030200-96033000	Strong transcription	Brain Angular Gyrus	brain
31	chr9:96030200-96033600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:96030200-96033600	Strong transcription	Left Ventricle	heart
33	chr9:96030200-96033800	Strong transcription	Colon Smooth Muscle	Colon
34	chr9:96030400-96033400	Strong transcription	Fetal Muscle Leg	muscle
35	chr9:96030400-96033400	Enhancers	Stomach Mucosa	stomach
36	chr9:96030600-96032600	Weak transcription	Brain Anterior Caudate	brain
37	chr9:96030600-96033400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr9:96031000-96032400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:96031200-96032800	Weak transcription	Spleen	Spleen
40	chr9:96031200-96033400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:96031400-96032400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr9:96031400-96032400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr9:96031400-96032400	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr9:96031400-96032800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:96031400-96033000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:96031400-96033000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:96031400-96033200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:96031400-96033600	Enhancers	Primary B cells from peripheral blood	blood
49	chr9:96031400-96037800	Weak transcription	Gastric	stomach
50	chr9:96031400-96054600	Weak transcription	Rectal Smooth Muscle	rectum

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