Variant report

Variant	rs12348239
Chromosome Location	chr9:116349360-116349361
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116348874..116350912-chr9:116362853..116364416,2	MCF-7	breast:
2	chr9:116344266..116346925-chr9:116348617..116352466,4	K562	blood:
3	chr9:116035093..116036761-chr9:116347708..116350133,2	K562	blood:
4	chr9:116037188..116039708-chr9:116347471..116350102,2	K562	blood:
5	chr9:116340242..116342448-chr9:116347885..116349539,2	MCF-7	breast:
6	chr9:116345877..116347394-chr9:116349148..116351921,2	K562	blood:
7	chr9:116282242..116284285-chr9:116348888..116351501,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176386	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000136875	Chromatin interaction

Extended variants
information (count: 176 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10116799	0.87[EUR][1000 genomes]
rs10125960	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10217341	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10481676	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10481677	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981789	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10981803	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981807	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981808	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981814	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981816	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981817	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981819	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981820	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981821	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981825	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981826	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981827	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981828	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981829	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981831	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981832	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981835	0.82[AFR][1000 genomes]
rs12335716	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12336719	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12337340	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12338588	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12338697	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12338701	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339493	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339501	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12339617	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12340996	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12341332	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341490	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12342508	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12342699	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12343129	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12343141	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12343940	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12344334	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12344578	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12345524	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12345968	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12346076	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12346087	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12346939	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12347895	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12348214	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12349661	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12353541	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1890992	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2050865	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2050866	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28594159	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28694002	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28714985	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35270441	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35358414	0.80[EUR][1000 genomes]
rs35533905	0.80[EUR][1000 genomes]
rs3983381	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41301525	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41305473	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41313331	0.87[EUR][1000 genomes]
rs4596719	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55676913	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55696921	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55777057	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55805468	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55931715	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55977108	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56155263	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56276438	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56390346	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61749208	0.96[EUR][1000 genomes]
rs6478011	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6478016	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6478022	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6478023	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7018783	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7020623	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7021688	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7023661	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7024445	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7024612	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7024996	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7025170	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7025745	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7026568	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7026656	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7027024	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7027340	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7028327	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7029685	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032311	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7037441	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7040031	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7041833	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7042290	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7042695	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7043140	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7043571	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7045347	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7046202	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7046427	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7047062	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048208	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048305	0.87[EUR][1000 genomes]
rs72760092	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72760093	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72760097	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72761903	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72761904	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72761966	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761968	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72761972	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72761982	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72761985	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761987	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761988	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72761992	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761994	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761997	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72762002	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763803	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72763804	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72763806	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763816	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763826	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763827	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763828	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763831	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763832	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763842	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763843	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72763848	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72763849	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72763851	0.80[EUR][1000 genomes]
rs7848203	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7849841	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7851718	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853373	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853792	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7854197	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7855325	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7856515	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7857943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7859047	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7860673	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7861248	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7863159	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864645	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7865364	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867353	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7870227	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7870451	0.89[EUR][1000 genomes]
rs7871186	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7872084	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7872192	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7872283	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs867375	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs884899	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299215	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs944345	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs944346	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9657641	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9657658	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9657659	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116337200-116349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:116338200-116353600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:116340200-116355400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:116341600-116355800	Weak transcription	Fetal Brain Female	brain
5	chr9:116341800-116353600	Weak transcription	A549	lung
6	chr9:116342000-116355400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:116342200-116349600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:116342200-116352200	Weak transcription	Fetal Kidney	kidney
9	chr9:116343200-116358800	Weak transcription	Hela-S3	cervix
10	chr9:116344600-116351000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:116344600-116351400	Strong transcription	Fetal Intestine Small	intestine
12	chr9:116344800-116351800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:116344800-116352400	Genic enhancers	Primary monocytes fromperipheralblood	blood
14	chr9:116344800-116352600	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr9:116344800-116353800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:116344800-116355400	Weak transcription	Small Intestine	intestine
17	chr9:116345000-116350600	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr9:116345200-116349800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:116345200-116349800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr9:116345200-116351000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:116345400-116349400	Strong transcription	Primary B cells from cord blood	blood
22	chr9:116345400-116349400	Strong transcription	Primary T cells from cord blood	blood
23	chr9:116345400-116349400	Weak transcription	Stomach Mucosa	stomach
24	chr9:116345400-116349800	Strong transcription	Colonic Mucosa	Colon
25	chr9:116345400-116350200	Strong transcription	Fetal Thymus	thymus
26	chr9:116345400-116350600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:116345600-116349400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:116345600-116349400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:116345600-116349800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr9:116345600-116350400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:116345600-116351000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr9:116345600-116351600	Genic enhancers	Lung	lung
33	chr9:116345600-116352200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr9:116345800-116350600	Genic enhancers	Pancreas	Pancrea
35	chr9:116346000-116350600	Genic enhancers	Spleen	Spleen
36	chr9:116346400-116350600	Strong transcription	GM12878-XiMat	blood
37	chr9:116346400-116351000	Genic enhancers	Gastric	stomach
38	chr9:116346400-116355200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:116346600-116349400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:116346600-116356800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:116346800-116351400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:116346800-116351400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:116346800-116353800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:116346800-116355800	Weak transcription	Brain Germinal Matrix	brain
45	chr9:116346800-116356000	Weak transcription	Ovary	ovary
46	chr9:116347000-116349800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:116347000-116353400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:116347000-116353600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:116347200-116349800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:116347200-116351200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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