Variant report

Variant	rs2322262
Chromosome Location	chr4:142575266-142575267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142296783..142297618-chr4:142574582..142575731,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10028670	0.90[EUR][1000 genomes]
rs1040257	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11100722	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100723	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100724	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508955	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13111860	0.87[EUR][1000 genomes]
rs1476326	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493024	0.86[EUR][1000 genomes]
rs1519550	0.86[EUR][1000 genomes]
rs1519552	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519553	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1589241	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607592	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607593	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850853	0.90[EUR][1000 genomes]
rs2087849	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2254514	0.87[EUR][1000 genomes]
rs4956404	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4956407	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6537058	0.95[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816210	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6837991	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841454	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs6842194	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661408	0.86[EUR][1000 genomes]
rs7665842	0.84[EUR][1000 genomes]
rs7688250	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs7698675	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683566	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684235	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970327	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970328	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990851	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2322262	MED9	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142565400-142580600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:142567800-142586400	Weak transcription	HSMM	muscle
3	chr4:142568800-142581000	Weak transcription	A549	lung
4	chr4:142569200-142577000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:142569200-142582800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:142570200-142579200	Weak transcription	Spleen	Spleen
7	chr4:142570400-142586400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:142570800-142578800	Weak transcription	GM12878-XiMat	blood
9	chr4:142573000-142575800	Enhancers	Fetal Stomach	stomach
10	chr4:142573400-142575600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:142573400-142575800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:142574000-142579000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:142574000-142579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:142574200-142586600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:142574800-142576200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:142574800-142576400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:142575000-142575600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:142575000-142575800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:142575000-142575800	Enhancers	HUVEC	blood vessel
20	chr4:142575200-142575400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:142575200-142575400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:142575200-142575400	Enhancers	Aorta	Aorta
23	chr4:142575200-142575400	Enhancers	Fetal Heart	heart
24	chr4:142575200-142575400	Enhancers	NH-A	brain
25	chr4:142575200-142575600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:142575200-142575600	Enhancers	Adipose Nuclei	Adipose
27	chr4:142575200-142575600	Enhancers	Right Atrium	heart
28	chr4:142575200-142575600	Enhancers	Small Intestine	intestine
29	chr4:142575200-142575600	Enhancers	NHDF-Ad	bronchial
30	chr4:142575200-142575600	Enhancers	NHLF	lung
31	chr4:142575200-142575600	Enhancers	Osteobl	bone
32	chr4:142575200-142575800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr4:142575200-142575800	Enhancers	Left Ventricle	heart
34	chr4:142575200-142575800	Enhancers	Psoas Muscle	Psoas

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