Variant report

Variant	rs56013900
Chromosome Location	chr1:247457537-247457538
allele	C/T
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	RCOR1	chr1:247457532-247458237	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247455319..247457914-chr1:247494277..247496616,2	MCF-7	breast:
2	chr1:247456054..247458907-chr1:247476595..247478143,2	K562	blood:
3	chr1:247456296..247458047-chr1:247490288..247491803,2	K562	blood:

Variant related genes	Relation type
ENSG00000202079	TF binding region
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10754545	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1192833	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12023326	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12023478	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026978	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027522	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034916	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12034919	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12035371	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12035515	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047860	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12048553	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404914	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17664745	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850825	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322048	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56335231	0.88[ASN][1000 genomes]
rs56366903	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56396334	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58522562	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6426239	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690864	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697861	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7522071	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56013900	ZNF496	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247449200-247462000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:247449400-247460800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:247449600-247462400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:247451000-247460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:247451600-247460400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:247452400-247460800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:247452600-247460800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:247452600-247461200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:247452800-247462000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:247453000-247460800	Weak transcription	Fetal Brain Female	brain
11	chr1:247453000-247462000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247453200-247460400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:247453400-247462000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:247453400-247463000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:247454200-247462600	Weak transcription	Pancreas	Pancrea
16	chr1:247454400-247457600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:247454400-247461800	Enhancers	Fetal Thymus	thymus
18	chr1:247454600-247458000	Enhancers	K562	blood
19	chr1:247454800-247458400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:247454800-247458400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:247454800-247459800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:247455000-247457800	Enhancers	Placenta	Placenta
23	chr1:247455000-247458400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:247455000-247460000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
26	chr1:247455200-247457800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:247455200-247460000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:247455200-247460200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:247455200-247461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:247455200-247463000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:247455400-247459800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:247455400-247461200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:247455600-247457800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr1:247455600-247459000	Enhancers	NH-A	brain
35	chr1:247455600-247462600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr1:247455800-247459000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:247455800-247459800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:247455800-247460800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:247455800-247462200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr1:247455800-247462600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:247455800-247464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:247456000-247462000	Weak transcription	Lung	lung
43	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
44	chr1:247456200-247459200	Enhancers	Osteobl	bone
45	chr1:247456200-247460800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:247456200-247462200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:247456600-247458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
49	chr1:247456800-247462000	Weak transcription	Ovary	ovary
50	chr1:247456800-247462200	Enhancers	HUES64 Cell Line	embryonic stem cell

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