Variant report

Variant	rs4657096
Chromosome Location	chr1:161713986-161713987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161454426..161456566-chr1:161713079..161714955,2	K562	blood:
2	chr1:161713367..161715023-chr1:161717731..161720555,2	MCF-7	breast:
3	chr1:161708205..161716175-chr1:161716206..161720292,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1027701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027702	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063178	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs10917821	0.81[EUR][1000 genomes]
rs12026445	0.88[CHB][hapmap]
rs12116756	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12121310	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs12121500	0.93[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12121522	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564653	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12745240	0.81[GIH][hapmap]
rs1340981	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417580	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1417581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2066247	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2174208	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657097	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657098	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427625	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427626	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7540096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv1005615	chr1:161707312-161714444	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4657096	PEAR1	cis	parietal	SCAN
rs4657096	SLAMF7	cis	parietal	SCAN
rs4657096	DUSP12	cis	lymphoblastoid	seeQTL
rs4657096	ARHGEF11	cis	cerebellum	SCAN
rs4657096	PEAR1	cis	cerebellum	SCAN
rs4657096	C1orf61	cis	cerebellum	SCAN
rs4657096	ETV3L	cis	cerebellum	SCAN
rs4657096	KCNJ9	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161706800-161718800	Weak transcription	NH-A	brain
2	chr1:161707600-161719200	Weak transcription	NHLF	lung
3	chr1:161711200-161714200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:161711400-161718800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:161711600-161717600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:161711600-161718600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:161713000-161714000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:161713000-161714200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:161713000-161714600	Enhancers	GM12878-XiMat	blood
10	chr1:161713000-161715400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:161713200-161714000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:161713200-161714000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:161713200-161714400	Enhancers	NHDF-Ad	bronchial
14	chr1:161713200-161715400	Enhancers	K562	blood
15	chr1:161713600-161714000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:161713600-161714000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:161713600-161714000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:161713600-161714000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:161713600-161714000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:161713600-161714000	Enhancers	HMEC	breast
21	chr1:161713600-161714200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:161713600-161714400	Enhancers	Osteobl	bone
23	chr1:161713600-161714600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:161713800-161714200	Enhancers	HUVEC	blood vessel
25	chr1:161713800-161714600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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