Variant report

Variant	rs2013878
Chromosome Location	chr15:58941236-58941237
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	chr15:58919702..58922554-chr15:58940056..58942110,2	K562	blood:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs16940570	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs16940574	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]
rs16940584	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs16940586	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs16940602	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16940614	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs16940638	0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs16940723	0.94[YRI][hapmap]
rs16940751	0.85[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap]
rs16953381	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs4277293	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs55939313	0.89[AFR][1000 genomes]
rs56039925	0.89[AFR][1000 genomes]
rs56357958	0.80[AFR][1000 genomes]
rs56942476	0.87[AFR][1000 genomes]
rs57083702	0.86[AFR][1000 genomes]
rs6494024	0.87[AFR][1000 genomes]
rs7164104	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs7166901	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7167240	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs7174279	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs7175610	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7176715	0.95[YRI][hapmap]
rs74016943	0.87[AFR][1000 genomes]
rs74016946	0.86[AFR][1000 genomes]
rs74016947	0.87[AFR][1000 genomes]
rs74017259	0.90[AFR][1000 genomes]
rs74017261	0.90[AFR][1000 genomes]
rs74017264	0.90[AFR][1000 genomes]
rs74017265	0.90[AFR][1000 genomes]
rs74017270	0.89[AFR][1000 genomes]
rs74017281	0.92[AFR][1000 genomes]
rs74017293	0.81[AFR][1000 genomes]
rs8025475	0.81[MKK][hapmap];1.00[TSI][hapmap]
rs8027618	0.88[AFR][1000 genomes]
rs8029869	0.85[ASW][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs8031250	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs8031412	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs8032451	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs8043275	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569602	chr15:58914326-58964437	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
3	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
4	chr15:58905600-58976400	Weak transcription	Gastric	stomach
5	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
6	chr15:58907800-58952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:58911600-58951200	Weak transcription	Fetal Brain Male	brain
8	chr15:58911600-58958000	Weak transcription	Fetal Brain Female	brain
9	chr15:58914200-58957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:58914600-58957000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:58919800-58959200	Weak transcription	Brain Germinal Matrix	brain
13	chr15:58920200-58946600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:58920200-58957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:58921000-58957600	Weak transcription	Colonic Mucosa	Colon
16	chr15:58921200-58946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:58921200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:58921200-58946800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:58921200-58949400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:58921200-58959600	Weak transcription	Aorta	Aorta
21	chr15:58921200-58968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:58921600-58942400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:58921600-58946600	Weak transcription	Fetal Intestine Small	intestine
24	chr15:58921600-58959200	Weak transcription	NHLF	lung
25	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
26	chr15:58921800-58946400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:58921800-58947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:58921800-58970400	Weak transcription	Stomach Mucosa	stomach
29	chr15:58922200-58959000	Weak transcription	HUVEC	blood vessel
30	chr15:58922400-58942600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:58923400-58942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:58923400-58971800	Weak transcription	Pancreas	Pancrea
33	chr15:58923400-58982800	Weak transcription	Lung	lung
34	chr15:58923800-58947400	Weak transcription	Fetal Stomach	stomach
35	chr15:58924000-58960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:58926400-58957600	Weak transcription	Brain Substantia Nigra	brain
37	chr15:58927000-58956600	Weak transcription	Ovary	ovary
38	chr15:58930000-58946600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:58931600-58946600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:58931800-58942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:58933000-58949600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:58933200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:58933200-58947000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:58933200-58952400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:58933400-58946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:58933400-58946600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:58933400-58946600	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:58933400-58947000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:58933400-58949800	Weak transcription	Hela-S3	cervix

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