Variant report

Variant	rs2520481
Chromosome Location	chr7:112064238-112064239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:111385127..111387426-chr7:112064078..112066608,2	MCF-7	breast:
2	chr7:112058693..112068099-chr7:112086961..112092875,22	MCF-7	breast:
3	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:
4	chr7:112060645..112065287-chr7:112088150..112093147,11	K562	blood:
5	chr7:112059129..112067568-chr7:112088387..112093703,18	K562	blood:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1015417	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1557698	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17492150	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs2396537	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2520468	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2520469	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2520472	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2520478	0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2520479	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2520480	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2520483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2520484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523036	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523043	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708591	0.85[ASN][1000 genomes]
rs2708593	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708599	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36113101	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6977129	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs727807	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs728273	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9640740	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs991632	0.97[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2520481	C7orf53	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112059800-112064400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:112061000-112064400	Enhancers	HMEC	breast
3	chr7:112061000-112089800	Weak transcription	Aorta	Aorta
4	chr7:112061200-112064400	Enhancers	Brain Substantia Nigra	brain
5	chr7:112061400-112064400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:112061600-112065400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:112061800-112064400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:112061800-112064600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:112061800-112065200	Enhancers	Fetal Thymus	thymus
10	chr7:112061800-112065800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr7:112062000-112064400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:112062000-112064400	Enhancers	Gastric	stomach
13	chr7:112062000-112064400	Enhancers	Pancreas	Pancrea
14	chr7:112062000-112064400	Flanking Active TSS	Dnd41	blood
15	chr7:112062000-112064400	Enhancers	Hela-S3	cervix
16	chr7:112062400-112064400	Enhancers	Primary hematopoietic stem cells	blood
17	chr7:112063200-112064400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr7:112063200-112064400	Enhancers	K562	blood
19	chr7:112063200-112066200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:112063400-112066200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:112063600-112064400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr7:112063600-112064600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr7:112063600-112066000	Enhancers	HepG2	liver
24	chr7:112063600-112070000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:112063800-112064400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr7:112063800-112064400	Active TSS	Primary B cells from cord blood	blood
27	chr7:112063800-112065600	Weak transcription	NH-A	brain
28	chr7:112064000-112064400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:112064000-112064400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:112064000-112064400	Enhancers	A549	lung
31	chr7:112064000-112064400	Enhancers	HSMMtube	muscle
32	chr7:112064000-112065400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr7:112064000-112066400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:112064000-112066400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:112064000-112067000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:112064000-112067400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr7:112064200-112064400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr7:112064200-112064400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:112064200-112064400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:112064200-112064400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:112064200-112064400	Enhancers	Thymus	Thymus
42	chr7:112064200-112065600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:112064200-112088400	Weak transcription	Psoas Muscle	Psoas

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