Variant report

Variant	rs2561526
Chromosome Location	chr5:100173257-100173258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10515265	1.00[EUR][1000 genomes]
rs10515266	1.00[EUR][1000 genomes]
rs1423381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159344	1.00[EUR][1000 genomes]
rs17159370	1.00[EUR][1000 genomes]
rs17159464	1.00[EUR][1000 genomes]
rs17159467	1.00[EUR][1000 genomes]
rs17159519	1.00[EUR][1000 genomes]
rs17159602	1.00[EUR][1000 genomes]
rs17159616	1.00[EUR][1000 genomes]
rs17159626	1.00[EUR][1000 genomes]
rs17160705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17160732	1.00[CEU][hapmap];0.98[AMR][1000 genomes]
rs17160844	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs17161136	0.87[AMR][1000 genomes]
rs2544911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2544914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544916	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2544917	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2548275	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2548277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561527	0.82[AMR][1000 genomes]
rs2725118	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776172	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs3776173	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3776179	0.84[ASN][1000 genomes]
rs3857364	1.00[EUR][1000 genomes]
rs6595534	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs6897681	1.00[EUR][1000 genomes]
rs73162282	0.84[ASN][1000 genomes]
rs73775624	1.00[EUR][1000 genomes]
rs768777	1.00[EUR][1000 genomes]
rs980901	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
3	chr5:100164000-100173800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:100164200-100174800	Weak transcription	Placenta	Placenta
5	chr5:100164200-100176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:100164400-100173600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:100164400-100175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:100164400-100175800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:100164600-100174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:100164600-100175000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:100165000-100173600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:100165000-100173600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:100165000-100174800	Weak transcription	Primary T cells from cord blood	blood
14	chr5:100165000-100175800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:100165000-100176200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:100165000-100176800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:100165600-100174200	ZNF genes & repeats	GM12878-XiMat	blood
18	chr5:100168800-100173400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:100168800-100176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:100169000-100173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:100170400-100174200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:100170600-100173600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:100170600-100179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:100170800-100173400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:100170800-100173800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:100171800-100173400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:100172000-100174200	Strong transcription	Primary B cells from cord blood	blood
28	chr5:100172400-100173400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:100172400-100173400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:100172400-100173800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr5:100172400-100176400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:100172600-100174000	Enhancers	Fetal Lung	lung
33	chr5:100172600-100174600	Strong transcription	Dnd41	blood
34	chr5:100173200-100173600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr5:100173200-100173800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr5:100173200-100173800	Genic enhancers	Monocytes-CD14+_RO01746	blood
37	chr5:100173200-100174000	Enhancers	A549	lung
38	chr5:100173200-100177000	Enhancers	HUVEC	blood vessel

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