Variant report

Variant	rs2354526
Chromosome Location	chr5:49949857-49949858
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	chr5:49949575..49951807-chr5:49954503..49956971,2	MCF-7	breast:

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10038842	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10039639	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10041633	0.82[EUR][1000 genomes]
rs10043477	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10052001	0.84[EUR][1000 genomes]
rs10065069	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10070517	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10471940	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10471956	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10755235	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10940424	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10940472	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10940497	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11738761	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11739828	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11741205	0.82[EUR][1000 genomes]
rs11745945	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11750241	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11750771	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12188262	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12188654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12519006	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12521579	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12653803	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12654776	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13153982	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13162921	0.81[EUR][1000 genomes]
rs13164951	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13173734	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359044	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13436520	0.88[ASN][1000 genomes]
rs1375127	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs152102	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154133	0.84[EUR][1000 genomes]
rs154134	0.81[ASN][1000 genomes]
rs154135	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154137	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154138	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154140	0.81[ASN][1000 genomes]
rs154141	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs157970	0.82[EUR][1000 genomes]
rs16884018	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs169497	0.81[ASN][1000 genomes]
rs171555	0.84[EUR][1000 genomes]
rs17195388	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs182230	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1823262	0.86[EUR][1000 genomes]
rs1823263	0.89[ASN][1000 genomes]
rs1839128	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1900738	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972980	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1988613	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2034392	0.80[EUR][1000 genomes]
rs2034393	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2034394	0.81[EUR][1000 genomes]
rs2121979	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2166893	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2166894	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2354525	0.88[ASN][1000 genomes]
rs2548581	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548582	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548583	0.83[EUR][1000 genomes]
rs256340	0.83[EUR][1000 genomes]
rs256341	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2594706	0.88[ASN][1000 genomes]
rs26065	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26066	0.84[EUR][1000 genomes]
rs26068	0.84[EUR][1000 genomes]
rs26069	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26071	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2697662	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs27244	0.82[EUR][1000 genomes]
rs27245	0.82[EUR][1000 genomes]
rs27251	0.82[EUR][1000 genomes]
rs27254	0.82[EUR][1000 genomes]
rs27357	0.81[EUR][1000 genomes]
rs27465	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27468	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27469	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27627	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27725	0.81[EUR][1000 genomes]
rs28085	0.81[EUR][1000 genomes]
rs282549	0.84[EUR][1000 genomes]
rs282550	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282551	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282552	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs282553	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282557	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282559	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs282561	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32376	0.81[ASN][1000 genomes]
rs32377	0.84[EUR][1000 genomes]
rs32378	0.84[EUR][1000 genomes]
rs32425	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763367	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39613	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4029420	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42284	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4282859	0.87[AFR][1000 genomes]
rs4440312	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4572006	0.84[ASN][1000 genomes]
rs4865628	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865895	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57079776	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62366937	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450292	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450359	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6863162	0.84[ASN][1000 genomes]
rs6867590	0.87[AFR][1000 genomes]
rs6868550	0.92[ASN][1000 genomes]
rs6869356	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6872070	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6872496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6879306	0.82[EUR][1000 genomes]
rs6886872	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6887758	0.84[ASN][1000 genomes]
rs6888147	0.84[EUR][1000 genomes]
rs6890519	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6890869	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7449019	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7702541	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7705837	0.86[ASN][1000 genomes]
rs7709831	0.84[EUR][1000 genomes]
rs7710150	0.84[EUR][1000 genomes]
rs7711839	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7721050	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7728222	0.82[EUR][1000 genomes]
rs7730847	0.82[EUR][1000 genomes]
rs7734389	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7736142	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs895801	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs921210	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv964851	chr5:49945480-49952101	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49949000-49951200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:49949200-49951800	Enhancers	Primary B cells from cord blood	blood
3	chr5:49949400-49950200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr5:49949400-49950200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr5:49949400-49950200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:49949400-49950200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr5:49949400-49950600	Enhancers	GM12878-XiMat	blood
8	chr5:49949400-49951200	Enhancers	Primary B cells from peripheral blood	blood
9	chr5:49949400-49951200	Enhancers	Primary hematopoietic stem cells	blood
10	chr5:49949400-49951600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:49949600-49950000	Enhancers	Primary T cells from cord blood	blood
12	chr5:49949600-49950000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr5:49949600-49950000	Enhancers	Thymus	Thymus
14	chr5:49949600-49950200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:49949600-49950200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:49949600-49951000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:49949600-49951000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:49949600-49952800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr5:49949800-49950000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr5:49949800-49950200	Enhancers	Fetal Thymus	thymus
21	chr5:49949800-49950400	Enhancers	Dnd41	blood
22	chr5:49949800-49951000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:49949800-49961600	Weak transcription	H9 Cell Line	embryonic stem cell

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