Variant report

Variant	rs11239582
Chromosome Location	chr10:46141795-46141796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46135491..46137232-chr10:46139389..46142363,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10466245	0.90[LWK][hapmap]
rs10900229	0.90[LWK][hapmap];0.82[AFR][1000 genomes]
rs10900232	0.85[YRI][hapmap]
rs11239571	0.90[LWK][hapmap]
rs11239586	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12240643	0.84[AFR][1000 genomes]
rs12243845	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12244834	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs12250401	0.91[AFR][1000 genomes]
rs12255138	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12257537	0.90[LWK][hapmap]
rs12265175	0.87[ASN][1000 genomes]
rs12267385	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41365544	0.87[ASN][1000 genomes]
rs58820822	0.91[AFR][1000 genomes]
rs59390133	0.82[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11239582	RASSF4	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46096200-46142000	Weak transcription	Brain Anterior Caudate	brain
3	chr10:46098200-46153400	Weak transcription	HSMM	muscle
4	chr10:46100200-46142600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:46103400-46142200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr10:46104400-46151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:46106400-46142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr10:46106800-46142000	Weak transcription	Fetal Kidney	kidney
9	chr10:46106800-46146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr10:46107800-46141800	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:46107800-46142000	Weak transcription	Esophagus	oesophagus
12	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
13	chr10:46108200-46142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:46108400-46142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:46108400-46149400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:46108600-46149200	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:46108600-46155400	Weak transcription	Fetal Intestine Small	intestine
19	chr10:46108800-46142000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:46110200-46153800	Weak transcription	NH-A	brain
21	chr10:46110800-46156800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:46112200-46152400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:46118800-46142400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:46119800-46148200	Weak transcription	Colonic Mucosa	Colon
25	chr10:46120000-46157800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr10:46120200-46148400	Weak transcription	Small Intestine	intestine
27	chr10:46122200-46142000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr10:46122200-46154600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:46122200-46157200	Weak transcription	Gastric	stomach
30	chr10:46122400-46141800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr10:46122400-46142000	Weak transcription	Fetal Lung	lung
32	chr10:46122400-46142200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:46122400-46149000	Weak transcription	Brain Substantia Nigra	brain
34	chr10:46122400-46156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:46122600-46141800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:46122600-46142000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:46122600-46142000	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:46122600-46142000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:46122600-46142400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr10:46122600-46142400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr10:46122800-46142200	Weak transcription	Lung	lung
42	chr10:46123200-46141800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:46123200-46142200	Weak transcription	Aorta	Aorta
44	chr10:46123400-46142000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr10:46123600-46142000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr10:46123600-46142200	Weak transcription	Thymus	Thymus
47	chr10:46124400-46142200	Weak transcription	Fetal Heart	heart
48	chr10:46125200-46142200	Weak transcription	Left Ventricle	heart
49	chr10:46130800-46147600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:46131000-46143200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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