Variant report

Variant	rs12059368
Chromosome Location	chr1:62627241-62627242
allele	C/T
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:15)

rs_ID	r²[population]
rs10789103	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10789104	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10789105	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10889292	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10889294	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207909	0.80[ASN][1000 genomes]
rs11207914	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022641	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12040256	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12091837	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12562124	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57176838	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6684324	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6687095	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs976574	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
4	chr1:62605000-62631800	Weak transcription	Lung	lung
5	chr1:62606400-62628600	Weak transcription	Stomach Mucosa	stomach
6	chr1:62607000-62630000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:62608400-62643600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:62608800-62627400	Weak transcription	Fetal Kidney	kidney
9	chr1:62612400-62629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:62612400-62632600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:62613400-62636000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:62614400-62628400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:62614400-62628800	Weak transcription	Ovary	ovary
14	chr1:62615200-62629000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:62615200-62629400	Weak transcription	NHEK	skin
16	chr1:62616200-62628200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:62616200-62629400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:62616200-62631800	Weak transcription	Right Ventricle	heart
19	chr1:62617200-62632000	Weak transcription	HMEC	breast
20	chr1:62617800-62631600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:62618000-62628800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:62618200-62629200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:62618200-62629600	Weak transcription	Primary T cells from cord blood	blood
24	chr1:62618200-62629800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:62618400-62629400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:62618600-62629200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:62618600-62631400	Weak transcription	Gastric	stomach
28	chr1:62618600-62631800	Weak transcription	Pancreas	Pancrea
29	chr1:62618600-62637800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:62619600-62627400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:62621000-62631000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:62621000-62632600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:62621200-62628600	Weak transcription	Esophagus	oesophagus
34	chr1:62621200-62631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:62621200-62636600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:62622600-62638000	Weak transcription	Fetal Intestine Small	intestine
37	chr1:62625200-62631000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:62625600-62628200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:62625600-62628200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:62626000-62628200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:62626400-62628200	Strong transcription	Liver	Liver
42	chr1:62626600-62627600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:62626600-62628200	Strong transcription	Aorta	Aorta
44	chr1:62626600-62628200	Strong transcription	Left Ventricle	heart
45	chr1:62627000-62642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:62627200-62628200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:62627200-62628400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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