Variant report

Variant	rs2071438
Chromosome Location	chr17:45285474-45285475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45264884..45268790-chr17:45285196..45288860,4	K562	blood:
2	chr17:45264174..45269379-chr17:45283146..45288200,6	K562	blood:

Variant related genes	Relation type
ENSG00000004897	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12946597	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515751	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713494	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs1713495	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs188799	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221597	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221598	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221599	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221602	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3785875	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968309	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs701982	0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs764792	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071382	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8076808	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs858673	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858679	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs938904	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9905948	0.82[EUR][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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2071438	ACLY	cis	parietal	SCAN
rs2071438	DBF4B	cis	parietal	SCAN
rs2071438	NMT1	cis	cerebellum	SCAN
rs2071438	SOST	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45281000-45286000	Enhancers	Fetal Muscle Leg	muscle
2	chr17:45281000-45288400	Enhancers	Fetal Thymus	thymus
3	chr17:45282600-45286000	Enhancers	K562	blood
4	chr17:45282600-45287400	Weak transcription	Lung	lung
5	chr17:45282800-45285600	Weak transcription	Spleen	Spleen
6	chr17:45282800-45285800	Enhancers	Fetal Heart	heart
7	chr17:45283000-45285600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:45283000-45285800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:45283000-45286200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:45283000-45287400	Weak transcription	Fetal Lung	lung
11	chr17:45283000-45289600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:45283200-45286000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:45283400-45285600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr17:45283400-45285800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:45283400-45286000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:45283400-45286000	Weak transcription	Fetal Stomach	stomach
17	chr17:45283400-45286000	Weak transcription	Left Ventricle	heart
18	chr17:45283400-45286000	Weak transcription	Right Ventricle	heart
19	chr17:45283400-45286000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:45283400-45287000	Enhancers	Primary B cells from cord blood	blood
21	chr17:45283400-45287000	Enhancers	Primary B cells from peripheral blood	blood
22	chr17:45283400-45287400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:45283400-45287600	Weak transcription	Psoas Muscle	Psoas
24	chr17:45283400-45287800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:45283400-45288000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr17:45283600-45286000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:45283600-45286200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr17:45283600-45286400	Weak transcription	Fetal Brain Male	brain
29	chr17:45283600-45286600	Enhancers	GM12878-XiMat	blood
30	chr17:45283600-45287800	Weak transcription	Osteobl	bone
31	chr17:45283800-45286000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:45283800-45286200	Weak transcription	NHDF-Ad	bronchial
33	chr17:45284000-45286000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:45284000-45286000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:45284200-45285800	Weak transcription	HSMM	muscle
36	chr17:45284200-45286200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:45284400-45293400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr17:45284600-45285600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr17:45284600-45286000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:45284600-45286000	Weak transcription	Placenta	Placenta
41	chr17:45284800-45285800	Weak transcription	HSMMtube	muscle
42	chr17:45284800-45286000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:45285000-45286000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:45285000-45286000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr17:45285000-45286000	Weak transcription	Right Atrium	heart
46	chr17:45285000-45287400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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