Variant report

Variant	rs16940586
Chromosome Location	chr15:58897591-58897592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58888706..58891622-chr15:58895276..58897701,2	MCF-7	breast:
2	chr15:58890495..58893590-chr15:58895773..58898243,3	K562	blood:
3	chr15:58623131..58625818-chr15:58896837..58898652,2	MCF-7	breast:
4	chr15:58892060..58893645-chr15:58896803..58898412,2	MCF-7	breast:
5	chr15:58894443..58897022-chr15:58897229..58899718,3	K562	blood:

Variant related genes	Relation type
ENSG00000239100	Chromatin interaction
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs16940570	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940574	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940584	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940602	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940614	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940638	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16940723	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940751	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs16940766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940771	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953381	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2013878	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2414609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277293	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55939313	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56039925	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56357958	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56935364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56942476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57083702	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57845422	1.00[EUR][1000 genomes]
rs58667875	1.00[AMR][1000 genomes]
rs58937576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61678411	1.00[EUR][1000 genomes]
rs6494024	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7163948	1.00[EUR][1000 genomes]
rs7164104	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166901	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167240	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168066	1.00[EUR][1000 genomes]
rs7172673	1.00[EUR][1000 genomes]
rs7173048	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7174279	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7175610	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176715	0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74016920	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74016943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74016946	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74016947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017259	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017261	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017264	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017265	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017270	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74017281	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74017286	1.00[EUR][1000 genomes]
rs74017293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74017301	1.00[EUR][1000 genomes]
rs74018920	1.00[EUR][1000 genomes]
rs74021007	1.00[AMR][1000 genomes]
rs8025475	1.00[EUR][1000 genomes]
rs8027618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8028872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8029869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031250	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031412	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8032451	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8033613	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8043275	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs881117	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1551	chr15:58891639-58936580	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58878000-58898400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:58878000-58900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr15:58878000-58900000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:58878400-58897800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:58878400-58900200	Weak transcription	Brain Substantia Nigra	brain
6	chr15:58878600-58900200	Weak transcription	NHLF	lung
7	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:58882600-58904000	Weak transcription	Gastric	stomach
11	chr15:58882600-58907600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:58883000-58901800	Weak transcription	HUVEC	blood vessel
13	chr15:58883200-58900400	Weak transcription	Fetal Heart	heart
14	chr15:58883200-58904600	Strong transcription	HSMM	muscle
15	chr15:58883400-58900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:58884400-58902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:58885800-58906800	Weak transcription	Fetal Brain Male	brain
18	chr15:58886400-58899800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:58887200-58906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:58887400-58898200	Weak transcription	Brain Angular Gyrus	brain
21	chr15:58887600-58897600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:58887800-58905200	Weak transcription	Brain Germinal Matrix	brain
23	chr15:58888000-58906200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:58888400-58900400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:58888400-58920000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:58888600-58899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:58889000-58900200	Weak transcription	Right Ventricle	heart
28	chr15:58889200-58900400	Weak transcription	NH-A	brain
29	chr15:58889600-58902000	Weak transcription	HMEC	breast
30	chr15:58889600-58904600	Weak transcription	Colonic Mucosa	Colon
31	chr15:58889600-58905200	Weak transcription	Fetal Brain Female	brain
32	chr15:58889600-58919800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:58889800-58899200	Weak transcription	Hela-S3	cervix
34	chr15:58889800-58901400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:58889800-58918800	Weak transcription	Osteobl	bone
36	chr15:58889800-58921000	Weak transcription	Ovary	ovary
37	chr15:58890000-58901400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:58890000-58904400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:58890000-58906200	Weak transcription	Small Intestine	intestine
40	chr15:58890800-58905200	Weak transcription	Brain Anterior Caudate	brain
41	chr15:58891000-58900000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr15:58891000-58900400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:58891000-58906800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr15:58891200-58898600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:58891200-58898800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:58891200-58899000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:58891600-58897800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:58891800-58898800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:58892000-58902200	Weak transcription	A549	lung

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