Variant report

Variant	rs269232
Chromosome Location	chr7:140323822-140323823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140177738..140180621-chr7:140323233..140327044,4	MCF-7	breast:
2	chr7:140224000..140226834-chr7:140322770..140324470,2	MCF-7	breast:
3	chr7:140285688..140288608-chr7:140322285..140325056,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133606	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10279057	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10458275	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10952779	0.81[AMR][1000 genomes]
rs17621539	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs17621746	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17621775	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs269227	0.83[YRI][hapmap]
rs28498721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57021669	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1021133	chr7:140270797-140338653	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1029128	chr7:140293389-140335570	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs269232	ADCK2	cis	cerebellum	SCAN
rs269232	NDUFB2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140267800-140326000	Weak transcription	Gastric	stomach
2	chr7:140287600-140326000	Weak transcription	Fetal Brain Male	brain
3	chr7:140296000-140326000	Weak transcription	Fetal Heart	heart
4	chr7:140302200-140326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:140302400-140326200	Weak transcription	Fetal Brain Female	brain
6	chr7:140302800-140326000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:140307600-140326000	Weak transcription	Spleen	Spleen
8	chr7:140308400-140324000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:140310800-140326400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:140319200-140325800	Weak transcription	Brain Germinal Matrix	brain
11	chr7:140320600-140326000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:140320600-140326000	Weak transcription	Left Ventricle	heart
13	chr7:140320600-140326000	Weak transcription	Right Atrium	heart
14	chr7:140320800-140326200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:140320800-140326200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:140321600-140325600	Weak transcription	NHDF-Ad	bronchial
17	chr7:140321600-140326000	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:140321600-140326000	Weak transcription	Brain Substantia Nigra	brain
19	chr7:140321600-140326400	Genic enhancers	Fetal Stomach	stomach
20	chr7:140321800-140324200	Weak transcription	A549	lung
21	chr7:140321800-140325800	Weak transcription	HSMMtube	muscle
22	chr7:140321800-140326000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:140321800-140326000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:140322000-140324000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:140322000-140324200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:140322000-140324200	Weak transcription	HMEC	breast
27	chr7:140322400-140324400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:140322600-140324000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:140322600-140324200	Weak transcription	NHEK	skin
30	chr7:140322600-140324400	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr7:140322600-140324800	Genic enhancers	Fetal Muscle Leg	muscle
32	chr7:140322600-140325000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:140322800-140325000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:140322800-140325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:140322800-140327800	Weak transcription	Psoas Muscle	Psoas
36	chr7:140323000-140324200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:140323000-140324200	Weak transcription	Liver	Liver
38	chr7:140323000-140325200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr7:140323400-140324600	Enhancers	NHLF	lung
40	chr7:140323600-140324000	Enhancers	Colon Smooth Muscle	Colon
41	chr7:140323600-140324400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:140323600-140324400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:140323600-140324400	Enhancers	Fetal Kidney	kidney
44	chr7:140323600-140324600	Enhancers	Adipose Nuclei	Adipose
45	chr7:140323600-140324600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr7:140323600-140324600	Enhancers	Rectal Smooth Muscle	rectum
47	chr7:140323600-140325000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr7:140323600-140325000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:140323600-140326000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:140323600-140326800	Enhancers	Placenta Amnion	Placenta Amnion

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