Variant report

Variant	rs6776582
Chromosome Location	chr3:160072020-160072021
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1141023	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236389	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236452	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236487	0.94[EUR][1000 genomes]
rs17826161	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882128	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979160	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2029361	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2152424	0.88[ASN][1000 genomes]
rs2272489	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281166	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737214	0.88[ASN][1000 genomes]
rs41272955	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41272957	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4254702	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4434183	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679883	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679887	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679894	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680577	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680582	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680590	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55853078	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55930449	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56030166	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56051094	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322040	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806971	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154549	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154552	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154567	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154591	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154596	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154600	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154602	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155903	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155920	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155922	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155924	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622031	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6776582	HKDC1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:160025400-160073000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:160025600-160073200	Weak transcription	Left Ventricle	heart
4	chr3:160034800-160082800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:160049400-160090600	Weak transcription	NH-A	brain
6	chr3:160049800-160073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:160055800-160072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:160055800-160087800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:160056200-160075200	Weak transcription	HSMM	muscle
12	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:160056400-160073000	Weak transcription	Fetal Stomach	stomach
14	chr3:160056400-160082800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
16	chr3:160056600-160072600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:160056600-160073200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:160056600-160082400	Weak transcription	Fetal Lung	lung
19	chr3:160056600-160082800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:160056600-160083200	Weak transcription	Fetal Intestine Small	intestine
21	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:160057200-160072800	Weak transcription	Primary B cells from cord blood	blood
23	chr3:160057600-160072800	Weak transcription	Fetal Intestine Large	intestine
24	chr3:160058400-160088800	Weak transcription	Osteobl	bone
25	chr3:160058600-160073200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:160058800-160083200	Weak transcription	GM12878-XiMat	blood
27	chr3:160059000-160072200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:160059000-160072800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:160059400-160077200	Weak transcription	Lung	lung
30	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
31	chr3:160062000-160072800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:160062400-160072800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:160062800-160073400	Weak transcription	A549	lung
34	chr3:160063000-160074400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:160063400-160073600	Weak transcription	Pancreas	Pancrea
36	chr3:160063400-160094000	Weak transcription	Fetal Brain Female	brain
37	chr3:160064400-160077800	Weak transcription	Spleen	Spleen
38	chr3:160065000-160072800	Weak transcription	Ovary	ovary
39	chr3:160065000-160082800	Weak transcription	NHDF-Ad	bronchial
40	chr3:160065000-160091600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:160065200-160073200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:160065400-160072400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:160065400-160072800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:160066000-160073400	Weak transcription	Dnd41	blood
45	chr3:160066200-160086000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:160066400-160099200	Weak transcription	NHEK	skin
47	chr3:160066800-160083200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:160067000-160072200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:160067200-160072800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:160067800-160097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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