Variant report

Variant	rs9311502
Chromosome Location	chr3:53560321-53560322
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	chr3:53559435..53562395-chr3:53622216..53624896,2	MCF-7	breast:
2	chr3:53554926..53557918-chr3:53559741..53561416,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1547950	0.92[ASN][1000 genomes]
rs1547951	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs17053168	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774425	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs3774428	1.00[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs3774439	0.83[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs3774440	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs3774441	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821842	0.83[JPT][hapmap]
rs3821846	0.88[GIH][hapmap]
rs3821847	0.83[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs59422128	0.90[EUR][1000 genomes]
rs62251864	0.95[EUR][1000 genomes]
rs62251868	0.86[EUR][1000 genomes]
rs62251870	0.83[EUR][1000 genomes]
rs62251903	0.83[EUR][1000 genomes]
rs62251904	0.83[EUR][1000 genomes]
rs6764908	0.83[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs72957281	0.95[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9311502	SPCS1	cis	parietal	SCAN
rs9311502	GNL3	cis	cerebellum	SCAN
rs9311502	RNF123	cis	parietal	SCAN
rs9311502	DCP1A	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53552400-53568400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:53553400-53562800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:53554800-53560400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:53556800-53560800	Enhancers	Rectal Smooth Muscle	rectum
5	chr3:53557000-53560800	Enhancers	Fetal Stomach	stomach
6	chr3:53558200-53560400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr3:53559000-53560600	Genic enhancers	Fetal Intestine Small	intestine
8	chr3:53559200-53560400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:53559200-53563800	Weak transcription	Aorta	Aorta
10	chr3:53559400-53560400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:53559400-53560400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr3:53559400-53561000	Enhancers	Colon Smooth Muscle	Colon
13	chr3:53559600-53560400	Enhancers	Fetal Heart	heart
14	chr3:53559800-53560400	Enhancers	Fetal Muscle Leg	muscle
15	chr3:53559800-53560400	Enhancers	Ovary	ovary
16	chr3:53559800-53560400	Enhancers	Hela-S3	cervix
17	chr3:53559800-53560600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:53559800-53560800	Genic enhancers	Fetal Intestine Large	intestine
19	chr3:53560000-53560400	Enhancers	Fetal Muscle Trunk	muscle
20	chr3:53560000-53560400	Enhancers	Pancreas	Pancrea
21	chr3:53560000-53560400	Enhancers	Right Atrium	heart
22	chr3:53560000-53560400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:53560000-53560600	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:53560000-53561600	Genic enhancers	Fetal Lung	lung
25	chr3:53560200-53560400	Active TSS	Fetal Brain Male	brain
26	chr3:53560200-53560400	Enhancers	Lung	lung

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