Variant report

Variant	rs17279663
Chromosome Location	chr1:179861950-179861951
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17279559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279684	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279712	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370777	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370826	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370847	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652455	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425595	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17279663	CLEC4G	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
2	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
3	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
8	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
10	chr1:179853800-179863200	Strong transcription	Fetal Lung	lung
11	chr1:179854000-179865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
13	chr1:179854200-179863000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:179854200-179863000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:179854200-179866600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
17	chr1:179854600-179864800	Strong transcription	Fetal Intestine Large	intestine
18	chr1:179854800-179864200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:179855200-179864600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:179855600-179871600	Weak transcription	A549	lung
21	chr1:179856000-179866000	Strong transcription	Liver	Liver
22	chr1:179856200-179876800	Weak transcription	NHLF	lung
23	chr1:179857600-179864000	Strong transcription	Dnd41	blood
24	chr1:179857600-179864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:179857600-179864800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:179857600-179864800	Strong transcription	Adipose Nuclei	Adipose
27	chr1:179857600-179865000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:179857600-179866600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:179857600-179867400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:179857600-179870000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:179857600-179871600	Weak transcription	HSMM	muscle
32	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
33	chr1:179857800-179865000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:179858000-179866600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:179858200-179862000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:179858200-179864800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:179858200-179864800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:179858200-179865200	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:179858200-179865200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:179858200-179866000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:179858200-179866000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:179858200-179867200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:179858400-179864600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:179858400-179864600	Strong transcription	Fetal Thymus	thymus
45	chr1:179858400-179865800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:179858600-179862800	Strong transcription	Primary B cells from cord blood	blood
47	chr1:179858600-179863000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:179858600-179864800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:179858600-179865400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:179858600-179865800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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