Variant report

Variant	rs1857290
Chromosome Location	chr3:99434166-99434167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99429413..99432457-chr3:99433966..99437540,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1021102	0.80[YRI][hapmap]
rs1087198	0.91[YRI][hapmap]
rs1606481	0.93[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs1630555	0.85[ASN][1000 genomes]
rs1711557	0.93[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs506186	0.87[ASN][1000 genomes]
rs629120	0.93[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs651511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668668	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694429	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs704570	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs704573	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs7636447	0.82[YRI][hapmap]
rs792828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs792829	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792834	1.00[CHB][hapmap]
rs793445	0.82[YRI][hapmap]
rs793460	0.82[YRI][hapmap]
rs793461	0.82[YRI][hapmap]
rs793462	0.82[YRI][hapmap]
rs793463	0.82[YRI][hapmap]
rs793465	0.82[YRI][hapmap]
rs793466	0.82[YRI][hapmap]
rs793467	0.91[YRI][hapmap]
rs793494	0.91[YRI][hapmap]
rs793495	0.91[YRI][hapmap]
rs796977	0.91[YRI][hapmap]
rs809415	0.82[YRI][hapmap]
rs812657	0.90[YRI][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	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1857290	SENP7	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99411400-99439600	Weak transcription	NHEK	skin
2	chr3:99423800-99440000	Weak transcription	Adipose Nuclei	Adipose
3	chr3:99426600-99439800	Weak transcription	NHLF	lung
4	chr3:99427000-99434200	Genic enhancers	Muscle Satellite Cultured Cells	--
5	chr3:99428000-99439600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:99428200-99436800	Weak transcription	Ovary	ovary
7	chr3:99428200-99439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:99428200-99442800	Weak transcription	Aorta	Aorta
9	chr3:99428400-99439600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:99430600-99434800	Weak transcription	NH-A	brain
11	chr3:99431000-99436000	Enhancers	NHDF-Ad	bronchial
12	chr3:99432000-99434200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:99433000-99435200	Weak transcription	HUVEC	blood vessel
14	chr3:99433200-99435800	Weak transcription	HSMMtube	muscle
15	chr3:99433400-99434800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:99433400-99435400	Weak transcription	HSMM	muscle
17	chr3:99433400-99437200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:99433600-99436200	Genic enhancers	Osteobl	bone
19	chr3:99433600-99449200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:99434000-99435600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:99434000-99440000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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