Variant report

Variant	rs272516
Chromosome Location	chr1:86847955-86847956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493789	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747328	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10873777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873782	0.86[CEU][hapmap];0.86[YRI][hapmap]
rs1158505	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1182102	1.00[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs1334143	0.95[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1334145	0.91[CEU][hapmap];0.86[YRI][hapmap]
rs1334146	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1334147	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1334148	0.91[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs166626	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs166627	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17129078	0.83[ASN][1000 genomes]
rs175363	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs185655	0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap]
rs187971	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1931363	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2104962	0.82[AFR][1000 genomes]
rs2104963	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2151708	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2151709	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs272491	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272492	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272494	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272498	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272504	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272507	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs272510	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs272511	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765975	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs405424	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs410807	0.82[EUR][1000 genomes]
rs4288573	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs450927	0.81[EUR][1000 genomes]
rs452865	0.81[EUR][1000 genomes]
rs567133	0.82[EUR][1000 genomes]
rs569912	0.82[EUR][1000 genomes]
rs61804060	0.83[ASN][1000 genomes]
rs6695671	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527383	0.82[EUR][1000 genomes]
rs883200	0.91[EUR][1000 genomes];0.91[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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1793594	chr1:86833653-86858957	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
2	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:86820200-86854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:86820200-86854800	Weak transcription	HSMMtube	muscle
5	chr1:86820400-86848000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:86820400-86860200	Weak transcription	NHEK	skin
7	chr1:86820600-86848000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:86824000-86848200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:86836600-86860800	Weak transcription	Aorta	Aorta
10	chr1:86839800-86848200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:86840600-86848200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:86840600-86859600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:86840800-86848600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:86841000-86849000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:86841000-86849400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:86841000-86851400	Weak transcription	HMEC	breast
17	chr1:86841000-86854400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:86841000-86859800	Weak transcription	HSMM	muscle
19	chr1:86841600-86859800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:86841800-86855000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:86842400-86848200	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:86843400-86848000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:86843400-86855000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:86843400-86860800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:86843600-86858600	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:86843600-86859200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:86843600-86860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:86843600-86860800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:86843800-86849000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:86843800-86854000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:86844200-86848000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:86844400-86848000	Weak transcription	Primary B cells from cord blood	blood
33	chr1:86844400-86849200	Weak transcription	Left Ventricle	heart
34	chr1:86844600-86853400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:86844800-86855000	Weak transcription	Thymus	Thymus
36	chr1:86844800-86859200	Weak transcription	Brain Germinal Matrix	brain
37	chr1:86844800-86861000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:86845000-86848000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:86845000-86850800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:86845000-86853800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:86845000-86855000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:86845000-86859200	Weak transcription	NH-A	brain
43	chr1:86845000-86859400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:86845000-86860200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:86845000-86860600	Weak transcription	Fetal Thymus	thymus
46	chr1:86845000-86860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:86845200-86859400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:86845800-86851200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:86846400-86848200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:86846400-86848600	Flanking Active TSS	Dnd41	blood

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