Variant report

Variant	rs2553011
Chromosome Location	chr2:173779775-173779776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13030842	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1344591	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1991173	0.85[CEU][hapmap]
rs2553009	0.83[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2553013	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2676501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2676502	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173764400-173792600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:173769200-173792400	Weak transcription	Fetal Kidney	kidney
3	chr2:173772000-173786000	Weak transcription	Right Atrium	heart
4	chr2:173774000-173786000	Weak transcription	Lung	lung
5	chr2:173775000-173783400	Weak transcription	GM12878-XiMat	blood
6	chr2:173775600-173780200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:173777200-173788800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:173777400-173781600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:173777600-173781400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:173778400-173780600	Weak transcription	Thymus	Thymus
11	chr2:173779000-173781400	Weak transcription	Primary T cells from cord blood	blood
12	chr2:173779400-173780800	Weak transcription	Fetal Thymus	thymus
13	chr2:173779600-173779800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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