Variant report

Variant	rs11207909
Chromosome Location	chr1:62607786-62607787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10789103	0.90[ASN][1000 genomes]
rs10789104	0.91[ASN][1000 genomes]
rs10889289	0.82[ASN][1000 genomes]
rs10889292	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10889294	0.80[ASN][1000 genomes]
rs11207906	0.80[ASN][1000 genomes]
rs11207907	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs11207908	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11207914	0.80[ASN][1000 genomes]
rs12022641	0.89[ASN][1000 genomes]
rs12038790	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12040256	0.91[ASN][1000 genomes]
rs12059368	0.80[ASN][1000 genomes]
rs12071351	0.96[ASN][1000 genomes]
rs12091837	0.91[ASN][1000 genomes]
rs1989208	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57176838	0.92[ASN][1000 genomes]
rs6670099	0.88[CEU][hapmap];0.80[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs6680411	0.82[CEU][hapmap]
rs6680526	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs7547052	0.82[ASN][1000 genomes]
rs976574	0.80[ASN][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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11207909	FOXD3	cis	cerebellum	SCAN
rs11207909	ECAT11	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
5	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
9	chr1:62566800-62608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:62570200-62607800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:62575200-62608000	Weak transcription	Fetal Kidney	kidney
12	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
13	chr1:62576800-62607800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62580000-62611600	Weak transcription	Pancreas	Pancrea
15	chr1:62580200-62617200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:62584600-62607800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:62590800-62609400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:62593200-62607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:62593400-62617600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
23	chr1:62593800-62607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:62594400-62614800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:62595000-62612600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:62595200-62614200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:62595200-62625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:62595400-62614000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:62595600-62607800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:62595800-62608200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62596000-62614000	Weak transcription	Left Ventricle	heart
32	chr1:62596000-62617800	Weak transcription	Aorta	Aorta
33	chr1:62596200-62614200	Weak transcription	Ovary	ovary
34	chr1:62598600-62614000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:62598800-62612600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:62599000-62616000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:62599400-62609000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:62602800-62607800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:62602800-62614000	Weak transcription	HMEC	breast
40	chr1:62603000-62614200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:62603600-62609200	Weak transcription	NHEK	skin
42	chr1:62603800-62607800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:62603800-62613800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:62603800-62617200	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:62603800-62617400	Weak transcription	Gastric	stomach
46	chr1:62603800-62617800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:62604000-62614000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:62604000-62614000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:62604600-62617800	Weak transcription	Esophagus	oesophagus
50	chr1:62605000-62631800	Weak transcription	Lung	lung

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