Variant report

Variant	rs2259359
Chromosome Location	chr15:44819513-44819514
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44816431..44820503-chr15:44827840..44830603,4	K562	blood:
2	chr15:44819187..44820716-chr15:44824468..44826576,2	MCF-7	breast:
3	chr15:44510075..44512914-chr15:44817653..44819556,2	K562	blood:
4	chr15:44818388..44821592-chr15:44826607..44831713,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPG11-1	chr15:44819455-44819737	ENSG00000179523.4

Variant related genes	Relation type
ENSG00000104131	Chromatin interaction
ENSG00000179523	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2433347	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2556560	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv904180	chr15:44783700-44820054	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	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	chr15:44721000-44828000	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	chr15:44775800-44820200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:44778000-44827800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:44778000-44827800	Weak transcription	Psoas Muscle	Psoas
9	chr15:44779800-44824200	Weak transcription	Gastric	stomach
10	chr15:44779800-44827800	Weak transcription	Aorta	Aorta
11	chr15:44783200-44827800	Weak transcription	NHLF	lung
12	chr15:44783600-44828000	Weak transcription	HSMMtube	muscle
13	chr15:44790400-44827200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:44790800-44827800	Weak transcription	Small Intestine	intestine
15	chr15:44791800-44826800	Weak transcription	Brain Germinal Matrix	brain
16	chr15:44795000-44820400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr15:44795200-44820200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:44796200-44827200	Weak transcription	K562	blood
19	chr15:44796200-44827800	Weak transcription	Brain Anterior Caudate	brain
20	chr15:44796200-44828000	Weak transcription	Brain Substantia Nigra	brain
21	chr15:44796400-44827800	Weak transcription	Esophagus	oesophagus
22	chr15:44796400-44827800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:44797000-44828000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:44798800-44828000	Weak transcription	A549	lung
25	chr15:44800800-44828000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:44805400-44820200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:44806000-44820000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:44806000-44820200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:44806200-44819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:44806200-44820400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:44806600-44820000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:44807000-44820800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:44807400-44828200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:44807800-44827200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:44810600-44820000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:44810800-44819800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:44810800-44820200	Strong transcription	Liver	Liver
38	chr15:44812800-44819800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:44812800-44827800	Weak transcription	Spleen	Spleen
40	chr15:44814000-44820400	Strong transcription	NHDF-Ad	bronchial
41	chr15:44814000-44827600	Weak transcription	NH-A	brain
42	chr15:44814200-44820200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:44815000-44820000	Strong transcription	Adipose Nuclei	Adipose
44	chr15:44815000-44820200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:44815200-44827400	Weak transcription	Osteobl	bone
46	chr15:44815400-44826600	Weak transcription	Fetal Brain Female	brain
47	chr15:44815400-44827400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:44815800-44822400	Weak transcription	Fetal Stomach	stomach
49	chr15:44815800-44825000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:44815800-44827200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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