Variant report

Variant	rs11083433
Chromosome Location	chr19:38209301-38209302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38207479..38209787-chr19:38374295..38376201,2	MCF-7	breast:
2	chr19:37996176..37999146-chr19:38209174..38211289,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188227	Chromatin interaction
ENSG00000266916	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1060522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853710	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666172	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668796	0.87[EUR][1000 genomes]
rs11671953	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11673497	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1291	0.82[LWK][hapmap];1.00[YRI][hapmap]
rs16975299	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17246792	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28431170	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2891657	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34991303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55871826	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55913702	0.87[EUR][1000 genomes]
rs55950325	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108305	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62108351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508739	0.87[EUR][1000 genomes]
rs7249622	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253081	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7258385	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73037060	0.84[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	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
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11083433	ZNF573	cis	brain	seeQTL
rs11083433	ZNF573	cis	multi-tissue	Pritchard
rs11083433	AC012309.5	cis	Thyroid	GTEx
rs11083433	ZNF573	trans	brain	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38198800-38209400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38198800-38209800	Weak transcription	Esophagus	oesophagus
3	chr19:38199000-38209400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:38199000-38209400	Weak transcription	HSMM	muscle
5	chr19:38200400-38209400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:38200600-38209400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:38202600-38209400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:38203000-38209400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:38206000-38209400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:38206200-38209400	Weak transcription	Lung	lung
11	chr19:38206200-38209600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:38207200-38210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:38207400-38209400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:38208800-38209400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:38208800-38209400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr19:38208800-38209400	Enhancers	Fetal Heart	heart
17	chr19:38208800-38209600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:38208800-38209600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:38208800-38209600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:38208800-38209600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:38208800-38210200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:38208800-38210800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr19:38208800-38211000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:38208800-38211000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr19:38208800-38211000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:38208800-38211200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr19:38209000-38209400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:38209000-38209400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:38209000-38209400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr19:38209000-38209400	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr19:38209000-38209400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:38209000-38209400	Enhancers	Duodenum Mucosa	Duodenum
33	chr19:38209000-38209400	Enhancers	Stomach Mucosa	stomach
34	chr19:38209000-38209400	Transcr. at gene 5' and 3'	A549	lung
35	chr19:38209000-38209400	Flanking Active TSS	HepG2	liver
36	chr19:38209000-38209600	Enhancers	Primary B cells from cord blood	blood
37	chr19:38209000-38209600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr19:38209000-38209600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr19:38209000-38209600	Flanking Active TSS	HMEC	breast
40	chr19:38209000-38209800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr19:38209000-38210000	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr19:38209000-38210000	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr19:38209000-38210000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr19:38209000-38210000	Flanking Active TSS	Fetal Brain Female	brain
45	chr19:38209000-38210000	Enhancers	Small Intestine	intestine
46	chr19:38209000-38210000	Enhancers	Spleen	Spleen
47	chr19:38209000-38210200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:38209000-38210200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:38209000-38210200	Flanking Active TSS	Dnd41	blood
50	chr19:38209000-38210800	Active TSS	H1 Cell Line	embryonic stem cell

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