Variant report

Variant	rs8039808
Chromosome Location	chr15:49939846-49939847
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:49936634-49941675	K562	blood:	n/a	n/a
2	POLR2A	chr15:49937746-49941045	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:49934468..49937629-chr15:49939008..49941773,3	K562	blood:
2	chr15:49935570..49938221-chr15:49938905..49941859,4	K562	blood:
3	chr15:49934440..49937340-chr15:49937772..49940035,3	MCF-7	breast:
4	chr15:49926539..49929038-chr15:49939808..49941780,2	K562	blood:
5	chr15:49911752..49916656-chr15:49939453..49943978,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261597	TF binding region
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10220770	1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10220846	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519234	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519238	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1055135	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11539519	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13313447	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962666	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962668	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962670	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962676	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962680	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962690	1.00[GIH][hapmap]
rs16962697	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1911615	1.00[EUR][1000 genomes]
rs1911617	0.93[ASW][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1911618	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2202711	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs34212162	0.81[AFR][1000 genomes]
rs58889385	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59112029	0.90[AMR][1000 genomes]
rs59565793	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59749619	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59942223	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60640257	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171994	0.87[EUR][1000 genomes]
rs7175199	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7175805	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176306	0.80[YRI][hapmap]
rs7176887	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs731052	0.93[ASW][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs73391021	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391038	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391046	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406025	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73406036	0.80[AMR][1000 genomes]
rs73406046	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406051	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406052	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406056	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406060	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406069	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406085	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406091	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406098	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406100	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407903	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407904	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407908	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74012439	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74012441	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8027730	0.83[YRI][hapmap]
rs8028721	0.81[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap]
rs8030707	0.81[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap]
rs8033054	1.00[GIH][hapmap]
rs8041629	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041771	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs906420	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9652425	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Response to anti-depressant treatment in major depressive disorder	22041458	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8039808	EGR2	trans	brain	seeQTL
rs8039808	CCL3	trans	brain	seeQTL
rs8039808	PTGS2	trans	brain	seeQTL

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49918200-49942200	Weak transcription	GM12878-XiMat	blood
2	chr15:49919800-49940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:49920000-49940400	Weak transcription	A549	lung
4	chr15:49920800-49940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:49927000-49940000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:49928000-49940200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:49928200-49940400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:49928200-49940600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:49928200-49943000	Weak transcription	Lung	lung
10	chr15:49936600-49940400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:49936800-49940600	Weak transcription	Fetal Thymus	thymus
12	chr15:49937000-49940000	Weak transcription	Small Intestine	intestine
13	chr15:49937000-49941000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:49937000-49941400	Weak transcription	Brain Germinal Matrix	brain
15	chr15:49937200-49940200	Weak transcription	Dnd41	blood
16	chr15:49937400-49940400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:49937400-49940600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr15:49937400-49942200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:49938200-49942200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:49938400-49940800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:49938400-49942000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:49938400-49944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:49938400-49944600	Weak transcription	Ovary	ovary
24	chr15:49938400-49945400	Weak transcription	Fetal Heart	heart
25	chr15:49938600-49940600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:49938600-49940800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:49938600-49941000	Weak transcription	Fetal Kidney	kidney
28	chr15:49938800-49940000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:49938800-49940200	Weak transcription	Right Atrium	heart
30	chr15:49938800-49940400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:49938800-49946200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:49939000-49940000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:49939000-49940000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:49939000-49940400	Weak transcription	NHLF	lung
35	chr15:49939000-49941200	Weak transcription	Primary T cells from cord blood	blood
36	chr15:49939000-49941200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:49939000-49941400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:49939000-49943200	Weak transcription	Aorta	Aorta
39	chr15:49939000-49944400	Weak transcription	HSMMtube	muscle
40	chr15:49939000-49944600	Weak transcription	Osteobl	bone
41	chr15:49939000-49945000	Weak transcription	Left Ventricle	heart
42	chr15:49939200-49940000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:49939200-49941400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:49939200-49941400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:49939200-49941600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:49939600-49940200	Weak transcription	Hela-S3	cervix
47	chr15:49939600-49940600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:49939800-49942400	Weak transcription	NHDF-Ad	bronchial
49	chr15:49939800-49942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:49939800-49942800	Weak transcription	HSMM	muscle

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