Variant report

Variant	rs17123057
Chromosome Location	chr1:62555219-62555220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11207899	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12130050	1.00[JPT][hapmap]
rs12137401	1.00[JPT][hapmap]
rs17123032	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17123054	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123117	1.00[CEU][hapmap]
rs2499002	1.00[JPT][hapmap]
rs2666469	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs2760224	0.86[ASN][1000 genomes]
rs28430757	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60941191	0.89[AFR][1000 genomes]
rs74076521	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076522	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
3	chr1:62532600-62557400	Weak transcription	Spleen	Spleen
4	chr1:62532600-62568200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:62532600-62569200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:62532800-62569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:62534400-62555400	Weak transcription	Left Ventricle	heart
9	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:62536800-62557400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:62536800-62566000	Weak transcription	Gastric	stomach
12	chr1:62541600-62563000	Weak transcription	Lung	lung
13	chr1:62542400-62586800	Weak transcription	NHEK	skin
14	chr1:62542400-62587400	Weak transcription	HMEC	breast
15	chr1:62542600-62555400	Weak transcription	Fetal Heart	heart
16	chr1:62542600-62563000	Weak transcription	Aorta	Aorta
17	chr1:62543400-62569400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:62544000-62575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:62544400-62555600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:62545000-62574800	Weak transcription	Fetal Kidney	kidney
21	chr1:62545400-62555600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:62548200-62594000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:62549800-62555600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:62550000-62555600	Strong transcription	Fetal Intestine Large	intestine
27	chr1:62550000-62557000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
29	chr1:62550600-62558600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:62551000-62555400	Weak transcription	Right Atrium	heart
31	chr1:62551400-62576000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:62551800-62594200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
34	chr1:62552000-62555400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:62552000-62556000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:62552400-62555400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:62553000-62579000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:62553000-62582800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:62553200-62594200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:62553400-62579600	Weak transcription	Pancreas	Pancrea
41	chr1:62553600-62563000	Weak transcription	Fetal Intestine Small	intestine
42	chr1:62553600-62579600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:62554000-62556600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:62554200-62562800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:62554400-62565000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:62554400-62581600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:62554800-62555400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:62554800-62556000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr1:62554800-62557000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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