Variant report

Variant	rs11239583
Chromosome Location	chr10:46146042-46146043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11239572	1.00[MKK][hapmap]
rs11239573	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs11239580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34257967	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55654107	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55893855	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55895325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61854126	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61855804	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1050880	chr10:46091441-46160597	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv540588	chr10:46091441-46160597	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv895113	chr10:46134013-46167847	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv540589	chr10:46136345-46153760	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11239583	ZNF485	cis	parietal	SCAN
rs11239583	ANTXRL	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46098200-46153400	Weak transcription	HSMM	muscle
3	chr10:46104400-46151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:46106800-46146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
6	chr10:46108400-46149400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:46108600-46149200	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:46108600-46155400	Weak transcription	Fetal Intestine Small	intestine
10	chr10:46110200-46153800	Weak transcription	NH-A	brain
11	chr10:46110800-46156800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:46112200-46152400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:46119800-46148200	Weak transcription	Colonic Mucosa	Colon
14	chr10:46120000-46157800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr10:46120200-46148400	Weak transcription	Small Intestine	intestine
16	chr10:46122200-46154600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr10:46122200-46157200	Weak transcription	Gastric	stomach
18	chr10:46122400-46149000	Weak transcription	Brain Substantia Nigra	brain
19	chr10:46122400-46156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:46130800-46147600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:46133800-46157800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr10:46134800-46147600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:46137200-46167000	Weak transcription	Right Ventricle	heart
24	chr10:46137600-46149000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:46137600-46156600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:46137600-46167200	Weak transcription	Ovary	ovary
27	chr10:46138000-46148200	Weak transcription	Fetal Brain Female	brain
28	chr10:46138400-46156600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr10:46138600-46147400	Strong transcription	Primary T cells from cord blood	blood
30	chr10:46138600-46148000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr10:46139400-46148000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:46140600-46150200	Weak transcription	HepG2	liver
33	chr10:46141200-46147200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr10:46141600-46148200	Weak transcription	HUVEC	blood vessel
35	chr10:46141800-46148800	Strong transcription	Primary B cells from cord blood	blood
36	chr10:46142400-46158000	Weak transcription	A549	lung
37	chr10:46142600-46146600	Weak transcription	Fetal Heart	heart
38	chr10:46142800-46146600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:46142800-46148200	Weak transcription	Spleen	Spleen
40	chr10:46142800-46152200	Weak transcription	Thymus	Thymus
41	chr10:46142800-46155200	Weak transcription	Pancreas	Pancrea
42	chr10:46142800-46155600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr10:46142800-46156400	Weak transcription	Fetal Stomach	stomach
44	chr10:46142800-46156800	Weak transcription	Lung	lung
45	chr10:46142800-46167000	Weak transcription	Esophagus	oesophagus
46	chr10:46142800-46167000	Weak transcription	Psoas Muscle	Psoas
47	chr10:46142800-46167000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:46142800-46167200	Weak transcription	Aorta	Aorta
49	chr10:46143000-46154400	Weak transcription	Fetal Muscle Leg	muscle
50	chr10:46143000-46156200	Weak transcription	Fetal Muscle Trunk	muscle

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