Variant report

Variant	rs6689160
Chromosome Location	chr1:179891565-179891566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179890721..179893462-chr1:179922578..179925183,2	MCF-7	breast:
2	chr1:179889909..179891977-chr1:179899561..179901875,2	K562	blood:
3	chr1:179885300..179888007-chr1:179889040..179891794,2	MCF-7	breast:
4	chr1:179890511..179892011-chr1:179902778..179905230,2	MCF-7	breast:
5	chr1:179889749..179892017-chr1:179923918..179925424,2	MCF-7	breast:
6	chr1:179850249..179852659-chr1:179890266..179891877,2	MCF-7	breast:
7	chr1:179890847..179892932-chr1:179926143..179929567,3	K562	blood:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17279483	1.00[YRI][hapmap]
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];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279594	1.00[YRI][hapmap]
rs17279663	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]
rs17279684	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370777	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370826	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651052	1.00[YRI][hapmap]
rs4652455	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425595	0.87[AFR][1000 genomes];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
rs6689160	CLEC4G	trans	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
2	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
3	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:179875200-179891800	Strong transcription	Primary B cells from cord blood	blood
8	chr1:179877000-179891600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:179882000-179891600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:179886400-179891600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr1:179887200-179893400	Weak transcription	Pancreas	Pancrea
12	chr1:179887200-179897200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:179887400-179891600	Weak transcription	Spleen	Spleen
14	chr1:179887400-179892800	Weak transcription	Gastric	stomach
15	chr1:179887400-179894600	Weak transcription	HSMMtube	muscle
16	chr1:179887400-179897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
18	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
19	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
20	chr1:179887400-179900600	Weak transcription	Ovary	ovary
21	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:179887600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:179887600-179899400	Weak transcription	K562	blood
24	chr1:179887800-179892000	Weak transcription	Fetal Heart	heart
25	chr1:179887800-179892200	Weak transcription	Colonic Mucosa	Colon
26	chr1:179887800-179893000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:179888000-179891600	Weak transcription	NH-A	brain
29	chr1:179888000-179894600	Weak transcription	HMEC	breast
30	chr1:179888200-179892200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:179888200-179892400	Weak transcription	Fetal Brain Female	brain
32	chr1:179888600-179892000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:179888600-179892000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:179888600-179892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:179888600-179892800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:179888600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:179888600-179895600	Weak transcription	NHLF	lung
38	chr1:179888600-179897200	Weak transcription	Esophagus	oesophagus
39	chr1:179888600-179897200	Weak transcription	Fetal Intestine Large	intestine
40	chr1:179888600-179899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:179888800-179892000	Weak transcription	Fetal Lung	lung
42	chr1:179888800-179892400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:179888800-179894400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:179888800-179900600	Weak transcription	Adipose Nuclei	Adipose
45	chr1:179889000-179892000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:179889000-179899400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:179889200-179894200	Weak transcription	Hela-S3	cervix
48	chr1:179889200-179895000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:179889200-179899200	Weak transcription	HepG2	liver
50	chr1:179889400-179892200	Weak transcription	Fetal Thymus	thymus

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