Variant report

Variant	rs2042042
Chromosome Location	chr9:86298204-86298205
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	chr9:86293365..86298412-chr9:86320425..86323449,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10115799	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10119344	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10125432	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035274	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044175	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746718	0.95[ASN][1000 genomes]
rs10746719	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746720	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746721	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780621	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868040	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868044	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868045	0.95[ASN][1000 genomes]
rs11140209	0.82[ASN][1000 genomes]
rs1333863	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333865	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360685	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968216	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058912	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542775	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542776	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542803	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780995	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780997	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780998	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780999	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781000	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2781001	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781003	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811919	0.89[ASN][1000 genomes]
rs2811922	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811923	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811924	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2811925	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811926	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811927	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811928	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811929	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811930	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811931	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146741	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242623	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454364	0.82[ASN][1000 genomes]
rs4877263	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877796	0.82[ASN][1000 genomes]
rs4877798	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559737	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559739	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7023082	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039019	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7469301	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850944	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860614	0.82[ASN][1000 genomes]
rs7863266	0.81[ASN][1000 genomes]
rs7865296	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874980	0.95[ASN][1000 genomes]
rs944946	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961807	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
3	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr9:86269400-86298600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:86273600-86298600	Weak transcription	Stomach Mucosa	stomach
8	chr9:86273600-86299000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:86273800-86304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:86279800-86299200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:86281600-86298800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:86282000-86298800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr9:86282000-86299000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:86282000-86300000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr9:86283400-86299000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:86284800-86298800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:86289000-86304200	Weak transcription	Ovary	ovary
19	chr9:86289000-86308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
21	chr9:86291000-86299000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:86291400-86314400	Weak transcription	Fetal Heart	heart
23	chr9:86291600-86300600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:86292800-86308600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:86293600-86301200	Weak transcription	Aorta	Aorta
26	chr9:86293600-86301400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:86293600-86304200	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:86293600-86317000	Weak transcription	NHLF	lung
29	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:86294200-86298600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:86294200-86305800	Weak transcription	Spleen	Spleen
32	chr9:86294200-86314200	Weak transcription	Gastric	stomach
33	chr9:86294200-86315600	Weak transcription	Right Ventricle	heart
34	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:86295000-86301400	Weak transcription	Fetal Kidney	kidney
36	chr9:86295000-86308800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:86295000-86313600	Weak transcription	Lung	lung
38	chr9:86296000-86298800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:86296000-86300200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:86296000-86304000	Weak transcription	NHDF-Ad	bronchial
41	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
42	chr9:86296200-86316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:86296400-86303000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:86296400-86304200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr9:86296600-86298600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr9:86296600-86303800	Weak transcription	Brain Substantia Nigra	brain
47	chr9:86296800-86299800	Weak transcription	A549	lung
48	chr9:86296800-86299800	Weak transcription	Hela-S3	cervix
49	chr9:86296800-86301400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:86296800-86302200	Weak transcription	Stomach Smooth Muscle	stomach

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