Variant report

Variant	rs11239308
Chromosome Location	chr10:45493033-45493034
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:45490763-45493058	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:45491199-45493109	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr10:45489983-45493423	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:45490674-45493096	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:45428885..45431662-chr10:45490818..45493446,2	K562	blood:
2	chr10:45477430..45479163-chr10:45492834..45495746,2	K562	blood:
3	chr10:45466696..45473467-chr10:45492241..45499604,15	K562	blood:
4	chr10:45484647..45486660-chr10:45491733..45494393,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF22	TF binding region
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11239299	1.00[AMR][1000 genomes]
rs11239303	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239305	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11239306	1.00[AMR][1000 genomes]
rs11239307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239309	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239311	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239315	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239319	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239323	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239324	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239342	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11239343	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11239345	0.94[EUR][1000 genomes]
rs11239346	0.94[EUR][1000 genomes]
rs12354652	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12358699	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12359377	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12359697	0.97[EUR][1000 genomes]
rs12359954	1.00[AMR][1000 genomes]
rs17157322	0.97[EUR][1000 genomes]
rs2274888	1.00[CEU][hapmap]
rs35521977	1.00[AMR][1000 genomes]
rs3740092	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740093	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758399	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs3758400	1.00[AMR][1000 genomes]
rs41301599	1.00[AMR][1000 genomes]
rs41301601	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41301609	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301611	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41306544	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41306546	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59381196	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61269477	1.00[AMR][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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11239308	RASSF4	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45478800-45495800	Weak transcription	HMEC	breast
2	chr10:45482400-45495600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:45484200-45494200	Enhancers	Right Atrium	heart
4	chr10:45484600-45494200	Enhancers	Ovary	ovary
5	chr10:45485200-45493600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr10:45486000-45495600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:45486000-45495600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:45487200-45495600	Weak transcription	Brain Germinal Matrix	brain
9	chr10:45487200-45496200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:45487400-45495600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr10:45487800-45495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:45488200-45496000	Enhancers	Placenta	Placenta
13	chr10:45488400-45495800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:45488800-45495600	Enhancers	Primary hematopoietic stem cells	blood
15	chr10:45489000-45493200	Enhancers	NHDF-Ad	bronchial
16	chr10:45489200-45493600	Enhancers	HUVEC	blood vessel
17	chr10:45489200-45494200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:45489200-45494200	Enhancers	Lung	lung
19	chr10:45489200-45495200	Enhancers	Dnd41	blood
20	chr10:45489200-45495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:45489400-45495200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:45489400-45495400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:45489600-45495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:45489800-45493400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr10:45490000-45493200	Enhancers	Colon Smooth Muscle	Colon
26	chr10:45490000-45493600	Enhancers	Pancreas	Pancrea
27	chr10:45490000-45494000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:45490000-45495000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr10:45490000-45495600	Weak transcription	Fetal Brain Female	brain
30	chr10:45490000-45496000	Enhancers	Right Ventricle	heart
31	chr10:45490200-45493200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr10:45490200-45493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:45490200-45494200	Enhancers	Psoas Muscle	Psoas
34	chr10:45490200-45495400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr10:45490400-45493200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr10:45490400-45493400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr10:45490400-45493400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr10:45490400-45493400	Enhancers	Brain Hippocampus Middle	brain
39	chr10:45490400-45494000	Enhancers	Aorta	Aorta
40	chr10:45490400-45494600	Enhancers	Brain Anterior Caudate	brain
41	chr10:45490600-45493600	Enhancers	Brain Substantia Nigra	brain
42	chr10:45490600-45494000	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:45490800-45493200	Enhancers	Brain Angular Gyrus	brain
44	chr10:45490800-45493200	Enhancers	HSMMtube	muscle
45	chr10:45490800-45493600	Enhancers	Fetal Muscle Leg	muscle
46	chr10:45491000-45495800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr10:45491200-45495600	Enhancers	Osteobl	bone
48	chr10:45491200-45495800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:45491400-45495800	Enhancers	Left Ventricle	heart
50	chr10:45491600-45495600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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