Variant report

Variant	rs7520283
Chromosome Location	chr1:84558902-84558903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84551652..84556823-chr1:84558383..84561144,5	K562	blood:
2	chr1:84550027..84551748-chr1:84557212..84559116,2	MCF-7	breast:
3	chr1:84556236..84558984-chr1:84559547..84561523,2	MCF-7	breast:
4	chr1:84554743..84559247-chr1:84561300..84565476,7	K562	blood:

Variant related genes	Relation type
ENSG00000213540	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1021491	0.89[AMR][1000 genomes]
rs10493750	0.90[JPT][hapmap]
rs10782822	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10874427	0.84[MEX][hapmap]
rs11163897	0.84[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11163898	0.89[JPT][hapmap]
rs11163900	0.90[JPT][hapmap]
rs12132032	0.89[JPT][hapmap]
rs12404263	0.84[JPT][hapmap]
rs12405120	0.90[JPT][hapmap]
rs12724598	0.90[JPT][hapmap]
rs12746741	0.82[JPT][hapmap]
rs2250806	0.84[ASW][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs2792973	0.88[AMR][1000 genomes]
rs2792975	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs2792976	0.86[AMR][1000 genomes]
rs3861699	0.84[JPT][hapmap]
rs4907193	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674038	0.84[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6701486	0.81[GIH][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes]
rs6703653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs957828	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.90[AMR][1000 genomes];0.93[ASN][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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7520283	LOC339524	cis	cerebellum	SCAN
rs7520283	MCOLN2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84545000-84560600	Weak transcription	Fetal Lung	lung
2	chr1:84545000-84561200	Weak transcription	Ovary	ovary
3	chr1:84545000-84566800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:84545000-84570000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:84545200-84568600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:84545400-84560800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:84545800-84568600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:84546400-84560400	Weak transcription	Dnd41	blood
9	chr1:84552200-84561800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:84552200-84561800	Weak transcription	Right Atrium	heart
11	chr1:84552200-84569000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:84552600-84562000	Weak transcription	Fetal Stomach	stomach
13	chr1:84554600-84560000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:84555400-84559800	Weak transcription	NH-A	brain
15	chr1:84555400-84568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:84556400-84559600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:84556400-84559800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:84556400-84568400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:84556400-84568400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:84556400-84568400	Weak transcription	A549	lung
21	chr1:84556400-84568400	Weak transcription	HSMM	muscle
22	chr1:84556400-84569000	Weak transcription	Left Ventricle	heart
23	chr1:84556600-84561000	Weak transcription	HMEC	breast
24	chr1:84556600-84566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:84556600-84566600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:84556600-84568600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:84556800-84560400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:84557000-84559200	Weak transcription	Fetal Intestine Small	intestine
29	chr1:84558000-84560400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:84558000-84560400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:84558400-84559000	Active TSS	Pancreatic Islets	Pancreatic Islet

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