Variant report

Variant	rs3904958
Chromosome Location	chr1:180571635-180571636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180560503..180563331-chr1:180569688..180572566,2	K562	blood:
2	chr1:180523696..180527243-chr1:180568963..180571816,3	MCF-7	breast:
3	chr1:180570917..180573068-chr1:180574878..180576525,2	K562	blood:
4	chr1:180570381..180572417-chr1:180573841..180576525,3	K562	blood:
5	chr1:180568988..180574820-chr1:180577415..180583388,9	K562	blood:
6	chr1:180568131..180570344-chr1:180571002..180574160,3	K562	blood:
7	chr1:180560503..180562028-chr1:180571047..180572566,2	K562	blood:
8	chr1:180554771..180558903-chr1:180568895..180571854,4	K562	blood:

No data

No data

No data

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10798785	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3842895	0.88[MEX][hapmap];0.81[MKK][hapmap]
rs3843276	0.85[ASN][1000 genomes]
rs3843277	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6661105	1.00[CEU][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6701738	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9970145	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9970363	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3904958	MTX3	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180564400-180572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:180564800-180579600	Weak transcription	Right Atrium	heart
3	chr1:180568200-180572400	Weak transcription	Pancreas	Pancrea
4	chr1:180568200-180579800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:180568400-180572600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:180569000-180572800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:180569200-180572800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:180569800-180575400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:180571000-180573400	Enhancers	Left Ventricle	heart
10	chr1:180571200-180572200	Weak transcription	Fetal Heart	heart
11	chr1:180571400-180572400	Weak transcription	Right Ventricle	heart
12	chr1:180571400-180572400	Enhancers	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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