Variant report

Variant	rs11083428
Chromosome Location	chr19:38083967-38083968
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38077508..38079095-chr19:38083626..38085233,2	K562	blood:
2	chr19:38083796..38085329-chr19:38149997..38151871,2	MCF-7	breast:
3	chr19:38083812..38086216-chr19:38209948..38211806,2	MCF-7	breast:
4	chr19:38083351..38084930-chr19:38145695..38147583,2	K562	blood:
5	chr19:38083338..38085691-chr19:38270478..38272116,2	K562	blood:
6	chr19:38078147..38079812-chr19:38083382..38085459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120784	Chromatin interaction
ENSG00000198182	Chromatin interaction
ENSG00000189144	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11083427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1128327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11665759	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666738	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs11672440	0.87[CEU][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs12151280	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs12162238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460230	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12462271	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12462505	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1478462	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17303301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17305326	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2045911	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126976	0.92[ASN][1000 genomes]
rs2279150	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2290999	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs241952	0.80[CEU][hapmap]
rs241955	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35205379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59426132	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73031309	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73031321	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73031322	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73031326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033117	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033129	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033139	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73033145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73035158	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035164	0.96[EUR][1000 genomes]
rs73037036	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73039018	0.82[AMR][1000 genomes];0.85[EUR][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11083428	EIF3K	cis	parietal	SCAN
rs11083428	MRPS12	cis	cerebellum	SCAN
rs11083428	ZFP112	cis	parietal	SCAN
rs11083428	PLEKHG2	cis	cerebellum	SCAN
rs11083428	FOSB	cis	cerebellum	SCAN
rs11083428	CATSPERG	cis	parietal	SCAN
rs11083428	PSMC4	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38069800-38084600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:38072400-38084600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:38075200-38084600	Weak transcription	Fetal Heart	heart
4	chr19:38077200-38084600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:38078200-38084400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:38078200-38084600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:38078200-38084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:38078600-38084600	Weak transcription	Thymus	Thymus
9	chr19:38078800-38084600	Weak transcription	Colonic Mucosa	Colon
10	chr19:38079600-38084600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:38079600-38084600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:38080000-38084400	Weak transcription	Left Ventricle	heart
13	chr19:38080200-38084600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:38080400-38084600	Weak transcription	Small Intestine	intestine
15	chr19:38080600-38084400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:38081600-38084400	Weak transcription	Placenta	Placenta
17	chr19:38082000-38084000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:38082000-38084000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
19	chr19:38082400-38084400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:38082400-38084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:38082400-38084600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:38082400-38084600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:38082800-38084000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:38082800-38084600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:38083000-38084000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:38083000-38084600	Weak transcription	HSMMtube	muscle
27	chr19:38083200-38084000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr19:38083200-38084000	ZNF genes & repeats	Dnd41	blood
29	chr19:38083200-38084200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:38083200-38084600	Weak transcription	Primary T cells from cord blood	blood
31	chr19:38083200-38084600	Weak transcription	Fetal Stomach	stomach
32	chr19:38083400-38084000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
33	chr19:38083400-38084000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr19:38083600-38084000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
35	chr19:38083600-38084400	Weak transcription	Psoas Muscle	Psoas
36	chr19:38083600-38084600	Weak transcription	Fetal Kidney	kidney
37	chr19:38083600-38084600	Weak transcription	Ovary	ovary
38	chr19:38083600-38085400	ZNF genes & repeats	A549	lung
39	chr19:38083800-38084400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:38083800-38084600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:38083800-38084600	Weak transcription	Primary B cells from cord blood	blood
42	chr19:38083800-38084600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:38083800-38084600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr19:38083800-38084600	Weak transcription	Liver	Liver
45	chr19:38083800-38084600	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:38083800-38084600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:38083800-38084600	Weak transcription	Brain Substantia Nigra	brain
48	chr19:38083800-38084600	Weak transcription	Fetal Lung	lung
49	chr19:38083800-38084800	Weak transcription	Fetal Brain Male	brain

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