Variant report

Variant	rs347975
Chromosome Location	chr3:140291413-140291414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10755093	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10804675	0.87[GIH][hapmap];0.86[EUR][1000 genomes]
rs10935387	0.86[EUR][1000 genomes]
rs11714465	0.82[ASW][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11924925	0.82[EUR][1000 genomes]
rs12494698	0.85[GIH][hapmap];0.86[EUR][1000 genomes]
rs347973	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6762605	0.85[YRI][hapmap]
rs6775380	0.87[GIH][hapmap];0.86[EUR][1000 genomes]
rs6799764	0.87[GIH][hapmap];0.86[EUR][1000 genomes]
rs7631249	0.85[YRI][hapmap]
rs961554	0.85[YRI][hapmap]
rs9851873	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv870185	chr3:140265153-140395673	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	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
rs347975	TFDP2	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140286200-140292800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:140286200-140295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:140288400-140291600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:140288400-140291800	Weak transcription	Pancreas	Pancrea
5	chr3:140288600-140291600	Weak transcription	Liver	Liver
6	chr3:140288600-140291800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:140289000-140291800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:140290600-140292200	Enhancers	Right Atrium	heart
9	chr3:140290600-140293200	Enhancers	Left Ventricle	heart
10	chr3:140290800-140291800	Enhancers	Brain Substantia Nigra	brain
11	chr3:140290800-140292800	Enhancers	Right Ventricle	heart
12	chr3:140291000-140291800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:140291000-140292400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:140291400-140292200	Enhancers	Stomach Smooth Muscle	stomach
15	chr3:140291400-140293200	Strong transcription	HSMMtube	muscle
16	chr3:140291400-140294000	Enhancers	Ovary	ovary

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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