Variant report

Variant	rs1925342
Chromosome Location	chr1:67115230-67115231
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67110643..67112907-chr1:67115103..67117381,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10493411	0.86[CEU][hapmap]
rs10789211	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs10889638	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11208910	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs11208916	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs11208924	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11208929	0.83[AMR][1000 genomes]
rs11208930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs11208937	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12021913	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12023176	0.94[JPT][hapmap]
rs12039282	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs12041930	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs12046520	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12093843	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402181	0.83[AMR][1000 genomes]
rs1359461	0.92[YRI][hapmap]
rs1373909	0.94[JPT][hapmap]
rs6588209	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes]
rs6588214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686606	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs6701907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72918447	0.81[AMR][1000 genomes]
rs7525509	0.94[JPT][hapmap]
rs7526812	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535076	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs7537440	0.94[JPT][hapmap]
rs7547794	0.94[JPT][hapmap]
rs7547857	0.94[JPT][hapmap]
rs7551301	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes]
rs963140	0.94[JPT][hapmap]

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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1925342	SGIP1	cis	Whole Blood	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67090400-67155000	Weak transcription	Fetal Heart	heart
2	chr1:67091200-67128000	Weak transcription	NH-A	brain
3	chr1:67092000-67117200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:67099400-67115600	Weak transcription	Fetal Lung	lung
5	chr1:67100000-67144400	Weak transcription	Left Ventricle	heart
6	chr1:67102800-67120200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:67106200-67143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:67106800-67115800	Weak transcription	Fetal Brain Male	brain
9	chr1:67108000-67136200	Weak transcription	Fetal Brain Female	brain
10	chr1:67109000-67117800	Weak transcription	Osteobl	bone
11	chr1:67109200-67120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:67109200-67141800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:67109600-67134200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:67109600-67155000	Weak transcription	Brain Anterior Caudate	brain
15	chr1:67110200-67116400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:67110200-67118800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:67110800-67118400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:67110800-67134400	Weak transcription	Brain Substantia Nigra	brain
19	chr1:67111000-67120400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:67111000-67135200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:67111400-67154800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:67111800-67118200	Weak transcription	Aorta	Aorta
23	chr1:67114200-67115400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:67114200-67115400	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:67114200-67115400	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:67114200-67115400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:67114200-67116400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:67114200-67116400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:67114200-67134200	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:67114200-67142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:67114200-67156400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:67114400-67118200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:67114600-67142200	Weak transcription	NHLF	lung
34	chr1:67115200-67115600	Enhancers	Primary B cells from cord blood	blood
35	chr1:67115200-67116200	Enhancers	GM12878-XiMat	blood
36	chr1:67115200-67118000	Weak transcription	Fetal Kidney	kidney

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