Variant report

Variant	rs2609263
Chromosome Location	chr4:89829407-89829408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10001319	0.82[CHB][hapmap]
rs10001420	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs10019862	0.92[ASN][1000 genomes]
rs10028121	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10033435	0.88[ASN][1000 genomes]
rs10033476	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs1246630	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246633	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246637	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1246638	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246639	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1246641	0.96[ASN][1000 genomes]
rs1272570	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106968	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148439	0.92[ASN][1000 genomes]
rs1355836	0.80[ASN][1000 genomes]
rs1355837	0.80[ASN][1000 genomes]
rs1379934	1.00[CHB][hapmap]
rs1398937	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs1398938	0.87[ASN][1000 genomes]
rs1398939	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs1398941	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs1398943	0.80[ASN][1000 genomes]
rs1458552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513811	0.80[ASN][1000 genomes]
rs1513812	0.80[ASN][1000 genomes]
rs1513823	0.80[ASN][1000 genomes]
rs1533289	0.80[ASN][1000 genomes]
rs1563688	0.82[CHB][hapmap]
rs1708659	0.80[ASN][1000 genomes]
rs1708671	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs1708672	0.84[ASN][1000 genomes]
rs1708673	0.80[ASN][1000 genomes]
rs1708683	0.80[ASN][1000 genomes]
rs1795730	0.87[ASN][1000 genomes]
rs1795735	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs1795737	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs1795740	0.87[ASN][1000 genomes]
rs1828735	0.80[ASN][1000 genomes]
rs1903004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1903009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996139	0.80[ASN][1000 genomes]
rs2045516	0.96[ASN][1000 genomes]
rs2125410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446295	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446302	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2446309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464511	0.87[ASN][1000 genomes]
rs2464521	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2464527	0.86[AMR][1000 genomes]
rs2609254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2609274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2609278	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609281	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609284	0.88[ASN][1000 genomes]
rs2670618	0.80[ASN][1000 genomes]
rs2670619	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2670620	0.87[ASN][1000 genomes]
rs2670627	0.80[ASN][1000 genomes]
rs2670628	0.80[ASN][1000 genomes]
rs2704572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704580	0.84[ASN][1000 genomes]
rs2704585	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2704588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704591	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704592	0.80[ASN][1000 genomes]
rs2704593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704602	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704603	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28559811	0.87[ASN][1000 genomes]
rs28624770	0.92[ASN][1000 genomes]
rs28658282	0.92[ASN][1000 genomes]
rs2869965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869968	0.96[ASN][1000 genomes]
rs28718401	0.80[ASN][1000 genomes]
rs28869547	0.87[ASN][1000 genomes]
rs4498109	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59698155	0.92[ASN][1000 genomes]
rs6532100	0.80[ASN][1000 genomes]
rs6834297	0.80[ASN][1000 genomes]
rs7673427	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697878	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180333	0.80[ASN][1000 genomes]
rs922027	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938265	0.80[ASN][1000 genomes]
rs973680	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs993358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999793	0.87[ASN][1000 genomes]
rs9999873	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89820000-89859200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:89824600-89834000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:89825000-89831200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:89825600-89878400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:89826000-89832600	Weak transcription	Adipose Nuclei	Adipose
6	chr4:89826000-89839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:89826400-89838400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:89826600-89836200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:89827200-89837400	Weak transcription	Fetal Lung	lung
10	chr4:89827200-89847000	Weak transcription	Placenta	Placenta
11	chr4:89827400-89847000	Weak transcription	Ovary	ovary
12	chr4:89828000-89847000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:89828600-89830600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr4:89828800-89829600	Enhancers	HepG2	liver
15	chr4:89828800-89829800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr4:89828800-89830000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:89828800-89830200	Enhancers	Fetal Intestine Small	intestine
18	chr4:89829000-89829600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:89829000-89829600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr4:89829000-89829600	Enhancers	NHLF	lung
21	chr4:89829000-89830000	Enhancers	HSMMtube	muscle
22	chr4:89829000-89830200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:89829000-89830200	Enhancers	Fetal Intestine Large	intestine
24	chr4:89829000-89830200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr4:89829200-89829600	Weak transcription	Pancreas	Pancrea
26	chr4:89829200-89839400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:89829400-89829600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr4:89829400-89835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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