Variant report

Variant	rs12335716
Chromosome Location	chr9:116231220-116231221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116218884..116220525-chr9:116229994..116232111,2	MCF-7	breast:
2	chr9:116224048..116227995-chr9:116229141..116233391,10	MCF-7	breast:
3	chr9:116171144..116173742-chr9:116230694..116232545,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10116799	0.91[EUR][1000 genomes]
rs10125960	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10217341	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10481676	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10481677	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10981803	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981807	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981808	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981814	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981816	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981817	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981819	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981820	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981821	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981825	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981826	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981827	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981828	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10981829	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981831	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981832	0.87[EUR][1000 genomes]
rs12336719	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12337340	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12338588	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12338697	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12338701	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12339493	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12339501	1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12339617	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12340996	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12341332	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12341490	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12342508	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12342699	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12343129	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12343141	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12343940	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344334	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12344578	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12345524	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12345968	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12346076	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12346087	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12346939	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12347895	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12348214	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12348239	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12349661	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12353541	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1890992	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2050865	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2050866	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28594159	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28694002	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28714985	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35270441	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35358414	0.84[EUR][1000 genomes]
rs35533905	0.84[EUR][1000 genomes]
rs3983381	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41301525	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41305473	0.86[EUR][1000 genomes]
rs41313331	0.91[EUR][1000 genomes]
rs4596719	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55676913	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55696921	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55777057	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55805468	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55931715	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55977108	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56155263	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56276438	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56390346	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61749208	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6478011	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6478016	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6478022	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6478023	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7018783	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7020623	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7021688	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7023661	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7024445	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7024612	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7024996	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7025170	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7025745	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7026568	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7026656	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7027024	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7027340	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7028327	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7029685	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7032311	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7037441	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7040031	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7041833	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7042290	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7042695	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7043140	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7043571	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7045347	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7046202	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7046427	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7047062	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7048208	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7048305	0.91[EUR][1000 genomes]
rs72760092	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72760093	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72760097	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72761903	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72761904	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72761966	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72761972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72761982	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72761985	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72761987	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761988	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72761992	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761994	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761997	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72762002	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72763803	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763804	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72763806	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72763816	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72763826	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72763827	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72763828	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72763831	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72763832	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72763842	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72763843	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72763846	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72763848	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72763849	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7848203	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7849841	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7851718	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7853373	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7853792	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7854197	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7855325	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7856515	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7857943	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7859047	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7860673	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7861248	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7863159	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7864645	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7865364	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7867353	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7870227	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7870451	0.90[EUR][1000 genomes]
rs7871186	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7872084	0.85[EUR][1000 genomes]
rs7872192	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7872283	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs867375	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs884899	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9299215	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs944345	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs944346	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9657641	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9657658	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9657659	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116219400-116240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr9:116226600-116241400	Weak transcription	Lung	lung
3	chr9:116226800-116235200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:116226800-116241400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:116227000-116231400	Weak transcription	NHLF	lung
6	chr9:116227000-116232400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:116227000-116233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:116227400-116263800	Weak transcription	Colonic Mucosa	Colon
9	chr9:116228000-116236600	Weak transcription	Psoas Muscle	Psoas
10	chr9:116228200-116231400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:116228200-116231400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:116228200-116231400	Weak transcription	A549	lung
13	chr9:116228400-116233400	Weak transcription	Stomach Mucosa	stomach
14	chr9:116228400-116238200	Weak transcription	Fetal Intestine Small	intestine
15	chr9:116228400-116241400	Weak transcription	Fetal Thymus	thymus
16	chr9:116228400-116245000	Weak transcription	Fetal Intestine Large	intestine
17	chr9:116228600-116231400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:116228600-116233000	Enhancers	HepG2	liver
19	chr9:116228600-116236200	Weak transcription	Placenta	Placenta
20	chr9:116228600-116241400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr9:116228800-116231400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:116228800-116236000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:116230200-116231800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:116230600-116232000	Enhancers	Fetal Heart	heart
25	chr9:116230800-116232400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr9:116231000-116231400	Enhancers	Brain Cingulate Gyrus	brain
27	chr9:116231000-116231400	Active TSS	Fetal Muscle Trunk	muscle
28	chr9:116231000-116231600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:116231000-116231600	Enhancers	Aorta	Aorta
30	chr9:116231000-116231600	Enhancers	Brain Substantia Nigra	brain
31	chr9:116231000-116231600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr9:116231000-116231600	Enhancers	Fetal Stomach	stomach
33	chr9:116231000-116231600	Enhancers	Gastric	stomach
34	chr9:116231000-116231600	Enhancers	Left Ventricle	heart
35	chr9:116231000-116231600	Enhancers	Right Atrium	heart
36	chr9:116231000-116231600	Enhancers	Right Ventricle	heart
37	chr9:116231000-116231600	Enhancers	Stomach Smooth Muscle	stomach
38	chr9:116231000-116231600	Enhancers	Hela-S3	cervix
39	chr9:116231000-116231600	Enhancers	HSMM	muscle
40	chr9:116231000-116231800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:116231000-116231800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:116231000-116231800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:116231000-116231800	Enhancers	Brain Angular Gyrus	brain
44	chr9:116231000-116231800	Enhancers	Ovary	ovary
45	chr9:116231000-116231800	Enhancers	HSMMtube	muscle
46	chr9:116231000-116232400	Enhancers	Pancreas	Pancrea
47	chr9:116231200-116231800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:116231200-116231800	Enhancers	Brain Hippocampus Middle	brain
49	chr9:116231200-116232200	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:116231200-116232600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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