Variant report

Variant	rs3753812
Chromosome Location	chr1:180126141-180126142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180094856..180097003-chr1:180124933..180127557,2	K562	blood:
2	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
3	chr1:180123935..180126561-chr1:180199070..180201304,3	MCF-7	breast:
4	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
5	chr1:180051158..180053588-chr1:180124507..180126558,2	K562	blood:
6	chr1:180061211..180064450-chr1:180123630..180126274,3	MCF-7	breast:
7	chr1:180094624..180096269-chr1:180125316..180126971,2	MCF-7	breast:
8	chr1:179845447..179846955-chr1:180125305..180127512,2	K562	blood:
9	chr1:179850220..179853546-chr1:180124207..180127412,4	MCF-7	breast:
10	chr1:180075321..180078076-chr1:180124133..180126626,2	K562	blood:
11	chr1:180039217..180042128-chr1:180125172..180126963,2	K562	blood:
12	chr1:179922139..179925093-chr1:180123797..180126783,3	K562	blood:
13	chr1:180095863..180097872-chr1:180124437..180126586,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000121454	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10913934	0.84[AMR][1000 genomes]
rs12075337	0.88[LWK][hapmap]
rs35481032	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753800	0.80[ASN][1000 genomes]
rs3753805	0.84[LWK][hapmap];0.80[YRI][hapmap]
rs3767181	0.80[YRI][hapmap]
rs3767193	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767196	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767199	0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs3820311	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820312	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3845392	0.92[ASN][1000 genomes]
rs6689602	0.96[LWK][hapmap];0.90[YRI][hapmap]
rs7531169	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1011933	chr1:180125666-180171361	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753812	QSOX1	cis	Whole Blood	GTEx
rs3753812	QSOX1	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180124400-180126800	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr1:180124600-180126200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:180124600-180126200	Flanking Active TSS	K562	blood
4	chr1:180124600-180126400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:180124600-180126600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:180124600-180126600	Flanking Active TSS	NHEK	skin
7	chr1:180124600-180126800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr1:180124600-180127200	Flanking Active TSS	NH-A	brain
9	chr1:180124600-180129400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:180124800-180126800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:180124800-180127000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:180124800-180127000	Enhancers	Spleen	Spleen
13	chr1:180124800-180128000	Enhancers	Liver	Liver
14	chr1:180124800-180151000	Weak transcription	Aorta	Aorta
15	chr1:180125000-180126200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:180125000-180126200	Weak transcription	Small Intestine	intestine
17	chr1:180125000-180126600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:180125000-180126800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:180125000-180126800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:180125000-180126800	Flanking Active TSS	Fetal Brain Female	brain
21	chr1:180125000-180126800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:180125000-180127200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:180125000-180127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:180125000-180127400	Active TSS	Esophagus	oesophagus
25	chr1:180125000-180127600	Enhancers	Fetal Heart	heart
26	chr1:180125000-180127600	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:180125000-180128400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:180125000-180129400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:180125000-180133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:180125000-180136000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:180125200-180126200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr1:180125200-180126200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:180125200-180126200	Enhancers	Brain Germinal Matrix	brain
34	chr1:180125200-180126200	Enhancers	Dnd41	blood
35	chr1:180125200-180126400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:180125200-180126400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:180125200-180126800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:180125200-180126800	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:180125200-180126800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr1:180125200-180126800	Enhancers	Hela-S3	cervix
41	chr1:180125200-180126800	Enhancers	HSMMtube	muscle
42	chr1:180125200-180126800	Flanking Active TSS	NHDF-Ad	bronchial
43	chr1:180125200-180127000	Weak transcription	Psoas Muscle	Psoas
44	chr1:180125200-180127000	Enhancers	A549	lung
45	chr1:180125200-180127400	Flanking Active TSS	Osteobl	bone
46	chr1:180125200-180127600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:180125200-180128000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:180125200-180128200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:180125200-180129000	Enhancers	Gastric	stomach
50	chr1:180125200-180129600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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