Variant report

Variant	rs16940574
Chromosome Location	chr15:58887366-58887367
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58881400..58884258-chr15:58884787..58887600,3	K562	blood:
2	chr15:58758492..58760005-chr15:58885829..58888502,2	MCF-7	breast:
3	chr15:58874129..58875641-chr15:58886591..58888367,2	K562	blood:
4	chr15:58885619..58887532-chr15:58890942..58892494,2	K562	blood:
5	chr15:58886161..58889040-chr15:58891859..58893799,2	K562	blood:
6	chr15:58881180..58883026-chr15:58886491..58889151,2	K562	blood:

Variant related genes	Relation type
ENSG00000239100	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs16940570	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940584	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940586	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940602	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940614	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940638	0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16940723	0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16940751	0.85[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.89[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	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2013878	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[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	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167240	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];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	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176715	1.00[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]
rs8025475	0.85[MKK][hapmap];1.00[TSI][hapmap];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	0.85[ASW][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031250	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[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:2 , 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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58874600-58889200	Weak transcription	Small Intestine	intestine
2	chr15:58877600-58888200	Weak transcription	Placenta	Placenta
3	chr15:58877600-58888800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:58877800-58888400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:58877800-58889000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:58878000-58887600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:58878000-58887800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:58878000-58898400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:58878000-58900000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr15:58878000-58900000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:58878200-58889200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:58878200-58890800	Weak transcription	Spleen	Spleen
13	chr15:58878400-58887400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:58878400-58887600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:58878400-58888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:58878400-58890600	Weak transcription	Primary T cells from cord blood	blood
17	chr15:58878400-58897800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:58878400-58900200	Weak transcription	Brain Substantia Nigra	brain
19	chr15:58878600-58888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:58878600-58889000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:58878600-58889000	Weak transcription	K562	blood
22	chr15:58878600-58890600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:58878600-58900200	Weak transcription	NHLF	lung
24	chr15:58878800-58889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:58879200-58893800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:58880400-58888800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:58882600-58888200	Weak transcription	Hela-S3	cervix
31	chr15:58882600-58888400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:58882600-58888400	Weak transcription	HMEC	breast
33	chr15:58882600-58889600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:58882600-58904000	Weak transcription	Gastric	stomach
35	chr15:58882600-58907600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:58882800-58889000	Weak transcription	Fetal Lung	lung
37	chr15:58882800-58890000	Weak transcription	Fetal Intestine Small	intestine
38	chr15:58883000-58889400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:58883000-58889400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:58883000-58901800	Weak transcription	HUVEC	blood vessel
41	chr15:58883200-58900400	Weak transcription	Fetal Heart	heart
42	chr15:58883200-58904600	Strong transcription	HSMM	muscle
43	chr15:58883400-58887800	Weak transcription	A549	lung
44	chr15:58883400-58888000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:58883400-58888800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:58883400-58889000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:58883400-58890200	Weak transcription	Brain Anterior Caudate	brain
48	chr15:58883400-58893800	Weak transcription	Fetal Kidney	kidney
49	chr15:58883400-58900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:58883600-58888800	Weak transcription	Brain Hippocampus Middle	brain

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