Variant report

Variant	rs2555643
Chromosome Location	chr4:175459298-175459299
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10000806	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10009146	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10011444	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs17362255	0.81[EUR][1000 genomes]
rs2253349	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2253360	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2253442	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2262515	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555639	0.94[JPT][hapmap];0.82[AFR][1000 genomes]
rs2555642	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555672	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555673	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2555674	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56277334	0.99[ASN][1000 genomes]
rs62332188	0.90[ASN][1000 genomes]
rs6811079	0.91[ASN][1000 genomes]
rs6817069	0.93[ASN][1000 genomes]
rs6844275	0.91[ASN][1000 genomes]
rs9990951	0.94[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525487	chr4:175400104-175470867	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175449800-175460000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:175458800-175459600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:175458800-175459600	Enhancers	NHEK	skin
4	chr4:175458800-175461200	Enhancers	HepG2	liver
5	chr4:175458800-175461400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:175459000-175459800	Enhancers	Pancreas	Pancrea
7	chr4:175459000-175460000	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr4:175459000-175460000	Enhancers	A549	lung
9	chr4:175459000-175461200	Enhancers	HMEC	breast
10	chr4:175459000-175461400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:175459000-175461600	Enhancers	Placenta	Placenta
12	chr4:175459200-175459400	Enhancers	Liver	Liver
13	chr4:175459200-175459800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:175459200-175459800	Enhancers	Stomach Mucosa	stomach
15	chr4:175459200-175460000	Flanking Active TSS	GM12878-XiMat	blood
16	chr4:175459200-175460200	Enhancers	K562	blood
17	chr4:175459200-175461600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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