Variant report

Variant	rs11207899
Chromosome Location	chr1:62545404-62545405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10127514	1.00[ASN][1000 genomes]
rs10127819	1.00[ASN][1000 genomes]
rs17123054	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs17123057	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17123061	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17123117	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs28430757	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934216	1.00[ASN][1000 genomes]
rs41289432	1.00[ASN][1000 genomes]
rs58677444	1.00[ASN][1000 genomes]
rs58987719	1.00[ASN][1000 genomes]
rs60941191	1.00[ASN][1000 genomes]
rs74076514	1.00[ASN][1000 genomes]
rs74076516	1.00[ASN][1000 genomes]
rs74076518	1.00[ASN][1000 genomes]
rs74076520	1.00[ASN][1000 genomes]
rs74076521	0.92[EUR][1000 genomes]
rs74076522	0.92[EUR][1000 genomes]
rs74076523	1.00[ASN][1000 genomes]
rs74076524	1.00[ASN][1000 genomes]
rs74076525	1.00[ASN][1000 genomes]
rs74076528	0.96[EUR][1000 genomes]
rs74076530	0.96[EUR][1000 genomes]
rs74076548	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
4	chr1:62515400-62552400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:62519000-62550000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:62519000-62550000	Weak transcription	Pancreas	Pancrea
7	chr1:62519000-62552000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:62521800-62546200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:62532400-62552400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:62532600-62548800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:62532600-62550000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:62532600-62550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:62532600-62552400	Weak transcription	Esophagus	oesophagus
14	chr1:62532600-62557400	Weak transcription	Spleen	Spleen
15	chr1:62532600-62568200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:62532600-62569200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:62532800-62552800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:62532800-62569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:62533400-62550000	Weak transcription	Fetal Intestine Large	intestine
21	chr1:62534400-62555000	Weak transcription	Ovary	ovary
22	chr1:62534400-62555400	Weak transcription	Left Ventricle	heart
23	chr1:62536000-62554400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:62536200-62551000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:62536800-62557400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:62536800-62566000	Weak transcription	Gastric	stomach
28	chr1:62541600-62563000	Weak transcription	Lung	lung
29	chr1:62542000-62547200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:62542400-62550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62542400-62586800	Weak transcription	NHEK	skin
32	chr1:62542400-62587400	Weak transcription	HMEC	breast
33	chr1:62542600-62555400	Weak transcription	Fetal Heart	heart
34	chr1:62542600-62563000	Weak transcription	Aorta	Aorta
35	chr1:62543400-62551000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:62543400-62552800	Weak transcription	Brain Anterior Caudate	brain
37	chr1:62543400-62569400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:62543800-62550000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:62543800-62550200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:62544000-62575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:62544400-62555600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:62544600-62546000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:62544600-62548800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:62544600-62550000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:62544800-62545600	Strong transcription	Liver	Liver
46	chr1:62544800-62545600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:62544800-62553800	Weak transcription	HepG2	liver
48	chr1:62545000-62574800	Weak transcription	Fetal Kidney	kidney
49	chr1:62545200-62546800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:62545400-62546400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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