Variant report

Variant	rs2602489
Chromosome Location	chr11:77029738-77029739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77028301..77030747-chr11:77034393..77036479,2	K562	blood:
2	chr11:77022420..77024730-chr11:77028021..77030394,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224829	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10793246	0.82[ASN][1000 genomes]
rs10899365	0.82[ASN][1000 genomes]
rs10899368	0.82[ASN][1000 genomes]
rs10899369	0.82[ASN][1000 genomes]
rs10899376	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899378	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899379	0.86[EUR][1000 genomes]
rs11237145	0.81[ASN][1000 genomes]
rs11237146	0.81[ASN][1000 genomes]
rs11237147	0.81[ASN][1000 genomes]
rs11237154	0.82[ASN][1000 genomes]
rs11237173	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11237189	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11237193	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11237195	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237196	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11237199	0.80[EUR][1000 genomes]
rs12271542	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12287216	0.81[ASN][1000 genomes]
rs1377470	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1377471	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1453343	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1613357	0.82[ASN][1000 genomes]
rs1618188	0.82[ASN][1000 genomes]
rs1620915	0.82[ASN][1000 genomes]
rs1621624	0.82[ASN][1000 genomes]
rs1628438	0.82[ASN][1000 genomes]
rs1670451	0.82[ASN][1000 genomes]
rs1670452	0.82[ASN][1000 genomes]
rs1670453	0.82[ASN][1000 genomes]
rs1670454	0.84[ASN][1000 genomes]
rs17135625	0.90[ASN][1000 genomes]
rs1793469	0.84[ASN][1000 genomes]
rs1793470	0.84[ASN][1000 genomes]
rs1793488	0.81[ASN][1000 genomes]
rs1840151	0.88[EUR][1000 genomes]
rs1894214	0.82[ASN][1000 genomes]
rs1894215	0.82[ASN][1000 genomes]
rs1946005	0.82[ASN][1000 genomes]
rs2250639	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250647	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298793	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602458	0.88[EUR][1000 genomes]
rs2602459	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602463	0.81[EUR][1000 genomes]
rs2602464	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602465	0.90[EUR][1000 genomes]
rs2602468	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602469	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602470	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602472	0.91[EUR][1000 genomes]
rs2602477	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2602479	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2602488	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725810	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2725815	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725816	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2725819	0.81[ASN][1000 genomes]
rs2725826	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725827	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725830	0.88[EUR][1000 genomes]
rs2725831	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2725832	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729747	0.89[EUR][1000 genomes]
rs2729753	0.81[EUR][1000 genomes]
rs2729762	0.97[EUR][1000 genomes]
rs2729764	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2729769	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729771	0.81[EUR][1000 genomes]
rs2844328	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2844332	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844333	0.84[EUR][1000 genomes]
rs2844334	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844336	0.83[EUR][1000 genomes]
rs2844337	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852384	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2852385	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2852392	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2852394	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2853086	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2853087	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2853088	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2853090	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2853096	0.82[ASN][1000 genomes]
rs2853103	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28858991	0.82[EUR][1000 genomes]
rs3018424	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4590893	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7119033	0.86[EUR][1000 genomes]
rs7121984	0.81[ASN][1000 genomes]
rs7938075	0.81[ASN][1000 genomes]
rs9634031	0.82[ASN][1000 genomes]

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	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77020800-77032000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr11:77020800-77033200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:77021000-77032600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:77022400-77032000	Weak transcription	Fetal Intestine Large	intestine
5	chr11:77024800-77032000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:77025000-77033000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:77025000-77033000	Weak transcription	HSMMtube	muscle
8	chr11:77025000-77033000	Weak transcription	NHLF	lung
9	chr11:77025000-77033200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:77025000-77033200	Weak transcription	NHDF-Ad	bronchial
11	chr11:77025000-77033400	Weak transcription	NH-A	brain
12	chr11:77025000-77034200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:77025400-77033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:77025400-77037600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:77027400-77043000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:77027600-77033200	Weak transcription	Fetal Stomach	stomach
17	chr11:77027600-77043000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:77027800-77033400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:77028000-77032000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:77028000-77033000	Weak transcription	Fetal Intestine Small	intestine
21	chr11:77028000-77068400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:77028200-77033400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:77028200-77033400	Weak transcription	Liver	Liver
24	chr11:77028200-77066000	Weak transcription	Fetal Kidney	kidney
25	chr11:77028400-77043000	Weak transcription	Fetal Lung	lung
26	chr11:77029200-77033200	Weak transcription	Ovary	ovary
27	chr11:77029400-77032600	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links