Variant report

Variant	rs651009
Chromosome Location	chr9:98077892-98077893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98066646..98069496-chr9:98077286..98078854,2	K562	blood:
2	chr9:98059172..98061613-chr9:98077027..98078592,2	MCF-7	breast:
3	chr9:98054521..98056977-chr9:98076532..98078926,2	K562	blood:
4	chr17:40540218..40543029-chr9:98077707..98079432,2	MCF-7	breast:
5	chr9:98067922..98070273-chr9:98076676..98079113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230221	Chromatin interaction
ENSG00000168610	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1623009	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16905568	1.00[JPT][hapmap]
rs16909877	1.00[JPT][hapmap]
rs173339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs242448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs356662	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356663	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356671	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356685	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs400727	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes]
rs420089	0.80[EUR][1000 genomes]
rs4647379	1.00[MKK][hapmap]
rs4647513	1.00[MKK][hapmap];0.91[YRI][hapmap]
rs4743989	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744440	0.83[EUR][1000 genomes]
rs475413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs607105	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs648615	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7038007	0.80[AFR][1000 genomes]
rs9299427	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs651009	MIR23B	cis	lymphoblastoid	seeQTL
rs651009	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98075400-98078400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:98075400-98078600	Weak transcription	Stomach Mucosa	stomach
3	chr9:98075600-98078600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:98075600-98079000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:98075600-98079200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:98075800-98078200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:98075800-98078400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:98075800-98078600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:98075800-98078600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:98075800-98078600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr9:98075800-98078600	Weak transcription	Primary T cells from cord blood	blood
12	chr9:98075800-98078600	Weak transcription	Adipose Nuclei	Adipose
13	chr9:98075800-98078600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:98075800-98078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:98075800-98078600	Weak transcription	Brain Substantia Nigra	brain
16	chr9:98075800-98078600	Weak transcription	Colonic Mucosa	Colon
17	chr9:98075800-98078600	Weak transcription	Pancreas	Pancrea
18	chr9:98075800-98078600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:98075800-98078600	Weak transcription	Right Ventricle	heart
20	chr9:98075800-98078600	Weak transcription	Thymus	Thymus
21	chr9:98075800-98078600	Weak transcription	HSMM	muscle
22	chr9:98075800-98078600	Weak transcription	HSMMtube	muscle
23	chr9:98075800-98078800	Weak transcription	Placenta	Placenta
24	chr9:98075800-98078800	Weak transcription	Psoas Muscle	Psoas
25	chr9:98075800-98079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:98075800-98079000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:98075800-98079000	Weak transcription	Esophagus	oesophagus
28	chr9:98075800-98079000	Weak transcription	Left Ventricle	heart
29	chr9:98075800-98079000	Weak transcription	Ovary	ovary
30	chr9:98075800-98079200	Weak transcription	Gastric	stomach
31	chr9:98075800-98079200	Weak transcription	Small Intestine	intestine
32	chr9:98076000-98078000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:98076000-98078000	Weak transcription	Fetal Brain Female	brain
34	chr9:98076000-98078000	Weak transcription	Fetal Stomach	stomach
35	chr9:98076000-98078000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:98076000-98078000	Weak transcription	HMEC	breast
37	chr9:98076000-98078200	Weak transcription	Fetal Heart	heart
38	chr9:98076000-98078200	Weak transcription	Fetal Kidney	kidney
39	chr9:98076000-98078200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:98076000-98078400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:98076000-98078400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:98076000-98078400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:98076000-98078600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:98076000-98078600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:98076000-98078600	Weak transcription	Brain Anterior Caudate	brain
46	chr9:98076000-98078600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr9:98076000-98078600	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:98076000-98078600	Weak transcription	Colon Smooth Muscle	Colon
49	chr9:98076000-98078600	Weak transcription	Fetal Brain Male	brain
50	chr9:98076000-98078600	Weak transcription	Fetal Muscle Trunk	muscle

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