Variant report

Variant	rs12594320
Chromosome Location	chr15:73006950-73006951
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	chr15:73006465..73009251-chr15:73067136..73069749,2	K562	blood:
2	chr15:73002571..73004510-chr15:73005846..73007759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159322	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11072380	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs11072383	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072389	0.94[ASN][1000 genomes]
rs11856110	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12437473	0.94[ASN][1000 genomes]
rs12439200	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12439473	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591690	0.96[ASN][1000 genomes]
rs12898814	0.86[CHD][hapmap];0.83[GIH][hapmap]
rs12902361	0.93[ASN][1000 genomes]
rs12906007	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12916236	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916448	0.84[ASN][1000 genomes]
rs1346165	0.96[CHD][hapmap];0.89[GIH][hapmap];0.81[ASN][1000 genomes]
rs16957257	0.93[ASN][1000 genomes]
rs16957297	0.96[CHD][hapmap];0.83[ASN][1000 genomes]
rs2304598	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28562097	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28648660	0.94[ASN][1000 genomes]
rs28737436	0.94[ASN][1000 genomes]
rs28801790	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28827493	0.94[ASN][1000 genomes]
rs28866048	0.83[ASN][1000 genomes]
rs34660767	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4777541	0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6495017	0.83[ASN][1000 genomes]
rs6495018	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs7162166	0.84[CHB][hapmap]
rs7170394	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7172397	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175918	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7182854	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8023358	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8024644	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8026559	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs8031691	0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8036269	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][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	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv3430383	chr15:72821093-73035167	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12594320	NR2E3	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72979200-73023600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:72979200-73023600	Weak transcription	Lung	lung
3	chr15:72979400-73027200	Weak transcription	Aorta	Aorta
4	chr15:72979600-73023200	Weak transcription	Fetal Kidney	kidney
5	chr15:72979600-73026800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:72979800-73007200	Weak transcription	Left Ventricle	heart
7	chr15:72979800-73027400	Weak transcription	Hela-S3	cervix
8	chr15:72980200-73008000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:72981000-73018600	Weak transcription	Pancreas	Pancrea
10	chr15:72985200-73021000	Weak transcription	Fetal Intestine Small	intestine
11	chr15:72993000-73028800	Weak transcription	NHEK	skin
12	chr15:72999000-73009600	Weak transcription	HSMMtube	muscle
13	chr15:72999000-73020400	Weak transcription	NH-A	brain
14	chr15:72999000-73021800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:72999000-73044000	Weak transcription	Small Intestine	intestine
16	chr15:72999600-73027600	Weak transcription	NHLF	lung
17	chr15:72999800-73007600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:73000800-73007600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:73001200-73007400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:73001200-73027600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:73001400-73020400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:73001400-73027400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:73001400-73027400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:73001400-73027600	Weak transcription	Right Ventricle	heart
25	chr15:73001600-73007600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:73001600-73008600	Weak transcription	Placenta	Placenta
27	chr15:73001600-73018600	Weak transcription	HepG2	liver
28	chr15:73001800-73027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:73001800-73027400	Weak transcription	K562	blood
30	chr15:73001800-73033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:73002000-73007600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:73002000-73054600	Weak transcription	Fetal Brain Male	brain
33	chr15:73002200-73007600	Weak transcription	Thymus	Thymus
34	chr15:73002200-73023000	Weak transcription	Fetal Thymus	thymus
35	chr15:73002200-73026000	Weak transcription	Fetal Heart	heart
36	chr15:73002200-73028800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:73002400-73010600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:73002400-73022800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:73002400-73028800	Weak transcription	Psoas Muscle	Psoas
40	chr15:73002800-73007400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:73003000-73018600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:73003000-73027400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:73003000-73028800	Weak transcription	Dnd41	blood
44	chr15:73003000-73031400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:73003200-73007000	Weak transcription	A549	lung
46	chr15:73003200-73007200	Weak transcription	GM12878-XiMat	blood
47	chr15:73003200-73009400	Weak transcription	Brain Angular Gyrus	brain
48	chr15:73003200-73027800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:73003200-73029000	Weak transcription	Esophagus	oesophagus
50	chr15:73003400-73023000	Weak transcription	Colonic Mucosa	Colon

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