Variant report

Variant	rs1060522
Chromosome Location	chr19:38211056-38211057
allele	A/G
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	CTCF	chr19:38209103-38211671	A549	lung:	n/a	chr19:38210746-38210762 chr19:38210351-38210364 chr19:38209349-38209357 chr19:38210802-38210810
2	MAX	chr19:38209957-38211076	HCT-116	colon:	n/a	n/a
3	SIX5	chr19:38210239-38211226	A549	lung:	n/a	n/a
4	MAX	chr19:38210523-38211100	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr19:38210183-38211167	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr19:38210191-38211063	ECC-1	luminal epithelium:	n/a	chr19:38210357-38210367
7	E2F6	chr19:38209891-38211229	A549	lung:	n/a	chr19:38210677-38210686 chr19:38210397-38210406 chr19:38210304-38210316 chr19:38210614-38210623 chr19:38210305-38210316
8	TCF12	chr19:38209925-38211097	A549	lung:	n/a	chr19:38210357-38210367
9	MAX	chr19:38209966-38211117	MCF-7	breast:	n/a	n/a
10	MAX	chr19:38209892-38211100	A549	lung:	n/a	n/a
11	ZEB1	chr19:38210215-38211114	HepG2	liver:	n/a	n/a
12	TBP	chr19:38210490-38211076	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr19:38209544-38211137	A549	lung:	n/a	n/a
14	REST	chr19:38209645-38211120	H1-neurons	neurons:	n/a	chr19:38210527-38210545
15	CTCF	chr19:38209534-38211105	SK-N-SH	brain:	n/a	chr19:38210746-38210762 chr19:38210351-38210364 chr19:38210802-38210810
16	MAX	chr19:38210020-38211114	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37996176..37999146-chr19:38209174..38211289,2	MCF-7	breast:
2	chr19:38083812..38086216-chr19:38209948..38211806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267552	TF binding region
ZNF607	TF binding region
ENSG00000171817	Chromatin interaction
ENSG00000266916	Chromatin interaction
ENSG00000180479	Chromatin interaction
ENSG00000188227	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10853710	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666172	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.85[ASN][1000 genomes]
rs11673497	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16975299	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17246792	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28431170	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2891657	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34991303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55871826	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[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];1.00[ASN][1000 genomes]
rs62108305	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62108351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508739	0.87[EUR][1000 genomes]
rs7249622	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253081	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258385	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73037060	0.84[EUR][1000 genomes];0.81[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1060522	AC012309.5	cis	Thyroid	GTEx
rs1060522	ZNF573	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38208800-38211200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:38209200-38211200	ZNF genes & repeats	Liver	Liver
3	chr19:38209800-38211200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:38209800-38211200	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr19:38209800-38211200	Active TSS	Stomach Smooth Muscle	stomach
6	chr19:38210000-38211200	Active TSS	Brain Anterior Caudate	brain
7	chr19:38210000-38211200	Active TSS	Brain Cingulate Gyrus	brain
8	chr19:38210000-38211200	Active TSS	Fetal Brain Female	brain
9	chr19:38210000-38211200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr19:38210000-38211200	Active TSS	A549	lung
11	chr19:38210200-38211200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:38210200-38211200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:38210200-38211200	Active TSS	Adipose Nuclei	Adipose
14	chr19:38210600-38211200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:38210600-38211200	Flanking Active TSS	Dnd41	blood
16	chr19:38210800-38229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:38211000-38211200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr19:38211000-38211200	Enhancers	Fetal Heart	heart
19	chr19:38211000-38219000	Weak transcription	Ovary	ovary
20	chr19:38211000-38222000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:38211000-38224600	Weak transcription	Fetal Stomach	stomach
22	chr19:38211000-38225200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:38211000-38225200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:38211000-38226400	Weak transcription	Psoas Muscle	Psoas
25	chr19:38211000-38227600	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:38211000-38228400	Weak transcription	Fetal Muscle Leg	muscle
27	chr19:38211000-38228600	Weak transcription	Brain Substantia Nigra	brain
28	chr19:38211000-38229200	Weak transcription	Fetal Kidney	kidney
29	chr19:38211000-38229200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr19:38211000-38229200	Weak transcription	Left Ventricle	heart
31	chr19:38211000-38229400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:38211000-38229400	Weak transcription	Brain Germinal Matrix	brain
33	chr19:38211000-38229400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:38211000-38230200	Weak transcription	Hela-S3	cervix

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