Variant report

Variant	rs4579760
Chromosome Location	chr1:152141674-152141675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152140753..152142610-chr1:152144905..152147472,2	MCF-7	breast:
2	chr1:152019214..152020970-chr1:152140994..152143680,3	MCF-7	breast:
3	chr1:152134203..152137059-chr1:152140809..152145378,5	MCF-7	breast:
4	chr1:152140940..152143889-chr1:152152084..152153950,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10788821	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1131471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1131473	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11588437	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs12033735	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1496036	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496041	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2069258	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2496253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2935208	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999563	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3001974	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3001978	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007680	0.82[JPT][hapmap]
rs3122305	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3124316	0.95[JPT][hapmap]
rs4845419	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6700989	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs924087	0.88[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4579760	ADAMTSL4	cis	cerebellum	SCAN
rs4579760	BOLA1	cis	cerebellum	SCAN
rs4579760	THEM4	cis	cerebellum	SCAN
rs4579760	THEM4	cis	parietal	SCAN
rs4579760	LCE2D	cis	parietal	SCAN
rs4579760	S100A10	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152131400-152145800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:152134800-152142200	Enhancers	HMEC	breast
3	chr1:152137800-152142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:152138800-152141800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:152139400-152142200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:152139400-152142400	Enhancers	NHEK	skin
7	chr1:152139600-152141800	Enhancers	Hela-S3	cervix
8	chr1:152139600-152142200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:152139600-152142200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:152139600-152143200	Enhancers	Esophagus	oesophagus
11	chr1:152139800-152141800	Enhancers	Left Ventricle	heart
12	chr1:152139800-152141800	Enhancers	Osteobl	bone
13	chr1:152139800-152142000	Enhancers	A549	lung
14	chr1:152139800-152142200	Enhancers	NH-A	brain
15	chr1:152140000-152141800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
16	chr1:152140000-152142400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:152140000-152142400	Enhancers	Right Atrium	heart
18	chr1:152140400-152142200	Enhancers	Adipose Nuclei	Adipose
19	chr1:152140400-152143800	Enhancers	GM12878-XiMat	blood
20	chr1:152140600-152144200	Enhancers	Colon Smooth Muscle	Colon
21	chr1:152140800-152142200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:152141200-152142200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:152141200-152142800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:152141400-152141800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:152141400-152142800	Weak transcription	Spleen	Spleen
26	chr1:152141400-152143000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:152141600-152141800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:152141600-152141800	Bivalent Enhancer	HSMM	muscle
29	chr1:152141600-152142600	Enhancers	Skeletal Muscle Female	skeletal muscle

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