Variant report

Variant	rs2662283
Chromosome Location	chr5:90322028-90322029
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90321904..90323771-chr5:90678316..90680092,2	MCF-7	breast:
2	chr5:90314128..90316238-chr5:90320139..90322345,2	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10942624	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12186662	0.84[ASN][1000 genomes]
rs13179479	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13180409	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1819073	0.90[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1819074	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1828177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1828178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1848486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1848487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1852734	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1858070	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2010355	0.82[YRI][hapmap]
rs2048217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2367186	0.90[ASN][1000 genomes]
rs2367274	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2463775	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2662278	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2662279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2662280	0.95[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs2662281	0.99[ASN][1000 genomes]
rs2662282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2662284	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2697543	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2697544	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2697546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28875340	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4254936	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4454077	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6452930	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6452934	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6865615	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs689544	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7706034	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7719311	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7723511	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7733230	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs937920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998788	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90309800-90323200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90314800-90323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:90314800-90327000	Weak transcription	Gastric	stomach
4	chr5:90316600-90323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:90317000-90323200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:90317000-90325000	Enhancers	Colon Smooth Muscle	Colon
7	chr5:90317600-90324600	Enhancers	Stomach Mucosa	stomach
8	chr5:90317800-90323000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:90318400-90324200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:90318600-90323800	Weak transcription	K562	blood
11	chr5:90318800-90323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:90318800-90323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:90319200-90322200	Weak transcription	A549	lung
14	chr5:90319400-90323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:90319400-90324600	Enhancers	Fetal Lung	lung
16	chr5:90319600-90323200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:90319800-90324400	Enhancers	Fetal Stomach	stomach
18	chr5:90320200-90323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:90320600-90322200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr5:90320800-90322400	Enhancers	Fetal Intestine Large	intestine
21	chr5:90320800-90326800	Weak transcription	NHEK	skin
22	chr5:90321000-90322600	Enhancers	Duodenum Mucosa	Duodenum
23	chr5:90321000-90324000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:90321400-90323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:90321600-90322200	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:90321600-90322400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:90321600-90323000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:90321600-90324000	Enhancers	HepG2	liver
29	chr5:90321600-90325000	Enhancers	Liver	Liver
30	chr5:90321800-90323000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:90321800-90323200	Weak transcription	Adipose Nuclei	Adipose
32	chr5:90321800-90323200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:90322000-90322400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:90322000-90323200	Weak transcription	Small Intestine	intestine

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