Variant report

Variant	rs332863
Chromosome Location	chr19:38653097-38653098
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr19:38653047-38653837	A549	lung:	n/a	n/a
2	TCF12	chr19:38652871-38653998	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38651349..38653210-chr19:38716095..38718461,2	K562	blood:
2	chr19:38651241..38653210-chr19:38716095..38718461,3	K562	blood:

Variant related genes	Relation type
SIPA1L3	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10460171	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083447	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460188	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462587	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap]
rs12975576	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12984016	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12984380	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12984864	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985707	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545039	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1962866	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2004981	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010234	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2016074	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2116862	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2163817	0.86[EUR][1000 genomes]
rs2304132	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2382972	0.85[EUR][1000 genomes]
rs2382973	0.86[EUR][1000 genomes]
rs2569517	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332841	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs332845	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs332846	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs332854	0.85[EUR][1000 genomes]
rs332857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332859	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332860	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs332861	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332862	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34646932	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35467693	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35469521	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35972455	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852910	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3852911	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802248	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803805	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803808	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67910767	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71337549	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7253312	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253633	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258019	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100956	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107385	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855617	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs332863	EGLN2	cis	cerebellum	SCAN
rs332863	ERF	cis	cerebellum	SCAN
rs332863	MEGF8	cis	parietal	SCAN
rs332863	MARK4	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38643800-38654800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:38645600-38660800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:38646000-38661000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:38650800-38653800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr19:38651200-38653200	Strong transcription	Right Ventricle	heart
8	chr19:38651200-38653800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:38651200-38654000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:38651400-38653800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr19:38651400-38658400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:38652000-38653800	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr19:38652000-38654000	ZNF genes & repeats	Fetal Stomach	stomach
14	chr19:38652200-38653600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38652200-38653600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38652200-38653600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:38652200-38653800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:38652200-38653800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:38652200-38653800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:38652200-38653800	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr19:38652200-38653800	ZNF genes & repeats	A549	lung
22	chr19:38652200-38653800	ZNF genes & repeats	Dnd41	blood
23	chr19:38652400-38653200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:38652400-38653200	Enhancers	NHEK	skin
25	chr19:38652400-38653400	ZNF genes & repeats	GM12878-XiMat	blood
26	chr19:38652400-38653600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:38652400-38653600	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr19:38652400-38653600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
29	chr19:38652400-38653600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:38652400-38653600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
31	chr19:38652400-38653600	Strong transcription	Fetal Heart	heart
32	chr19:38652400-38653800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr19:38652400-38653800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
34	chr19:38652400-38653800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:38652400-38653800	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr19:38652400-38653800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
37	chr19:38652400-38653800	ZNF genes & repeats	Fetal Thymus	thymus
38	chr19:38652400-38653800	ZNF genes & repeats	Lung	lung
39	chr19:38652400-38653800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
40	chr19:38652400-38653800	ZNF genes & repeats	Thymus	Thymus
41	chr19:38652400-38653800	ZNF genes & repeats	Spleen	Spleen
42	chr19:38652400-38653800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
43	chr19:38652400-38654000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:38652400-38656400	Strong transcription	HepG2	liver
45	chr19:38652400-38657400	Strong transcription	Brain Angular Gyrus	brain
46	chr19:38652600-38653200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:38652600-38653200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:38652600-38653200	Strong transcription	Brain Anterior Caudate	brain
49	chr19:38652600-38653400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
50	chr19:38652600-38653400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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