Variant report

Variant	rs2556560
Chromosome Location	chr15:44821843-44821844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44820064..44823122-chr15:44832148..44835068,3	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16965650	0.82[ASW][hapmap];0.84[CEU][hapmap]
rs2259359	0.84[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2433347	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
3	esv3410956	chr15:44425145-44823647	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv904177	chr15:44582886-44821843	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv904179	chr15:44614684-44821843	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2556560	VPS39	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44721000-44828000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:44740600-44824600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:44750000-44827400	Weak transcription	Pancreas	Pancrea
4	chr15:44750200-44828000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:44757000-44827400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:44778000-44827800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:44778000-44827800	Weak transcription	Psoas Muscle	Psoas
8	chr15:44779800-44824200	Weak transcription	Gastric	stomach
9	chr15:44779800-44827800	Weak transcription	Aorta	Aorta
10	chr15:44783200-44827800	Weak transcription	NHLF	lung
11	chr15:44783600-44828000	Weak transcription	HSMMtube	muscle
12	chr15:44790400-44827200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:44790800-44827800	Weak transcription	Small Intestine	intestine
14	chr15:44791800-44826800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:44796200-44827200	Weak transcription	K562	blood
16	chr15:44796200-44827800	Weak transcription	Brain Anterior Caudate	brain
17	chr15:44796200-44828000	Weak transcription	Brain Substantia Nigra	brain
18	chr15:44796400-44827800	Weak transcription	Esophagus	oesophagus
19	chr15:44796400-44827800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:44797000-44828000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:44798800-44828000	Weak transcription	A549	lung
22	chr15:44800800-44828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:44807400-44828200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:44807800-44827200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr15:44812800-44827800	Weak transcription	Spleen	Spleen
26	chr15:44814000-44827600	Weak transcription	NH-A	brain
27	chr15:44815200-44827400	Weak transcription	Osteobl	bone
28	chr15:44815400-44826600	Weak transcription	Fetal Brain Female	brain
29	chr15:44815400-44827400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:44815800-44822400	Weak transcription	Fetal Stomach	stomach
31	chr15:44815800-44825000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:44815800-44827200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:44815800-44827200	Weak transcription	Ovary	ovary
34	chr15:44815800-44827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:44815800-44828000	Weak transcription	Fetal Kidney	kidney
36	chr15:44816000-44824200	Weak transcription	Lung	lung
37	chr15:44816000-44824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:44816000-44824600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:44816000-44827800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:44816200-44824000	Weak transcription	Fetal Intestine Small	intestine
41	chr15:44816400-44827800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:44816600-44824200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:44816600-44825000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:44816600-44826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:44816600-44827400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:44816600-44828000	Weak transcription	Brain Angular Gyrus	brain
47	chr15:44816600-44828000	Weak transcription	Thymus	Thymus
48	chr15:44816800-44827200	Weak transcription	HepG2	liver
49	chr15:44816800-44827400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:44816800-44827600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links