Variant report

Variant	rs1009477
Chromosome Location	chr10:49543152-49543153
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	chr10:49540878..49543802-chr10:49546206..49547724,2	K562	blood:
2	chr10:49540944..49543155-chr10:49549106..49551548,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11101291	0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11101297	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11101301	0.85[AMR][1000 genomes]
rs11101303	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11101315	0.85[AMR][1000 genomes]
rs11101316	0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11101319	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12241466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12241476	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12244705	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253926	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261651	0.95[YRI][hapmap]
rs12261653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12265885	1.00[AMR][1000 genomes]
rs12266878	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59115521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60051862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7070529	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs7100777	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv6587	chr10:49526329-49571804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49516400-49547200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:49516400-49559600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:49517800-49544600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:49518800-49544000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr10:49520200-49549800	Weak transcription	HUVEC	blood vessel
6	chr10:49522800-49550800	Weak transcription	Small Intestine	intestine
7	chr10:49525800-49551800	Weak transcription	Adipose Nuclei	Adipose
8	chr10:49526200-49552000	Weak transcription	NH-A	brain
9	chr10:49529000-49550800	Weak transcription	K562	blood
10	chr10:49530800-49554600	Weak transcription	Fetal Brain Male	brain
11	chr10:49535400-49548200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr10:49536800-49545200	Weak transcription	Brain Angular Gyrus	brain
13	chr10:49538400-49543200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr10:49538400-49543200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:49538600-49545400	Weak transcription	Hela-S3	cervix
16	chr10:49538600-49551400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:49538800-49544600	Weak transcription	Spleen	Spleen
18	chr10:49538800-49546600	Weak transcription	HSMMtube	muscle
19	chr10:49538800-49551200	Weak transcription	Brain Substantia Nigra	brain
20	chr10:49538800-49551400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:49539000-49551800	Weak transcription	NHLF	lung
22	chr10:49539200-49555000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:49539400-49548200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr10:49539600-49553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr10:49539800-49549800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr10:49540000-49543400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:49540400-49551200	Weak transcription	Ovary	ovary
28	chr10:49540400-49554000	Weak transcription	Pancreas	Pancrea
29	chr10:49540600-49549600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr10:49540600-49551800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:49540800-49544400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr10:49540800-49547800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:49540800-49551600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr10:49541000-49543200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:49541000-49543200	Strong transcription	Fetal Muscle Leg	muscle
36	chr10:49541000-49544600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:49541000-49545000	Weak transcription	Stomach Mucosa	stomach
38	chr10:49541000-49549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:49541000-49551800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr10:49541000-49551800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr10:49541000-49554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:49541200-49545400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr10:49541200-49546000	Weak transcription	Fetal Kidney	kidney
44	chr10:49541200-49551000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr10:49541200-49559400	Weak transcription	Fetal Lung	lung
46	chr10:49541400-49553800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr10:49541600-49543200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr10:49541600-49543800	Weak transcription	Placenta	Placenta
49	chr10:49541600-49544400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:49541600-49544800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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