Variant report

Variant	rs17279712
Chromosome Location	chr1:179877780-179877781
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179870344..179874512-chr1:179875182..179879064,5	K562	blood:
2	chr1:179877736..179879361-chr1:179907717..179909785,2	K562	blood:
3	chr1:179867675..179869971-chr1:179874720..179878392,3	K562	blood:
4	chr1:179870344..179873386-chr1:179876338..179880165,3	K562	blood:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000264916	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17279559	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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279663	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]
rs17279684	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370763	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370777	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370826	0.86[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652455	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689160	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
rs17279712	CLEC4G	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
2	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
7	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
8	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
9	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:179860400-179878800	Weak transcription	Colonic Mucosa	Colon
11	chr1:179861200-179878000	Weak transcription	Gastric	stomach
12	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:179861400-179882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:179861600-179886600	Weak transcription	Pancreas	Pancrea
15	chr1:179867200-179886600	Weak transcription	Small Intestine	intestine
16	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
17	chr1:179868200-179879800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:179868200-179880800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:179868400-179880600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:179868400-179880600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:179868400-179888800	Strong transcription	Adipose Nuclei	Adipose
24	chr1:179868400-179890600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:179868400-179890800	Strong transcription	Dnd41	blood
26	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:179868800-179889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:179868800-179889200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:179868800-179889600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:179869000-179879000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:179869000-179888200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:179869200-179879600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:179869200-179879600	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:179869200-179880400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:179869200-179881000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:179869200-179885600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:179869400-179880000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:179869400-179880400	Strong transcription	Osteobl	bone
41	chr1:179869400-179881000	Strong transcription	Colon Smooth Muscle	Colon
42	chr1:179869400-179889600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:179869400-179891400	Strong transcription	Liver	Liver
44	chr1:179869600-179880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:179870000-179890400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:179871200-179879200	Strong transcription	Fetal Intestine Small	intestine
47	chr1:179871200-179879800	Strong transcription	Fetal Thymus	thymus
48	chr1:179871200-179891000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:179871600-179880800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:179872000-179886600	Weak transcription	Brain Angular Gyrus	brain

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