Variant report

Variant	rs6684586
Chromosome Location	chr1:185114837-185114838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185113029..185115978-chr1:185116966..185118773,2	K562	blood:
2	chr1:185112945..185115248-chr1:185120909..185123637,2	MCF-7	breast:
3	chr1:185114068..185116270-chr1:185124385..185126877,5	MCF-7	breast:
4	chr1:185114176..185116855-chr1:185120494..185122664,2	K562	blood:
5	chr1:185113319..185116352-chr1:185124187..185127216,4	MCF-7	breast:
6	chr1:185035986..185038971-chr1:185111907..185115590,3	MCF-7	breast:
7	chr1:185112895..185116881-chr1:185123287..185126781,5	K562	blood:

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1008502	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10453829	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs10489579	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs10489581	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs1053166	0.81[TSI][hapmap]
rs10737256	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs10797999	1.00[CEU][hapmap]
rs10911674	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs10911679	0.82[TSI][hapmap]
rs12022419	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs12035073	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs12037692	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs12038919	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs12043427	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs12043495	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs12043617	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs12046095	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12408279	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs12409926	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1322646	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs1407554	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1407557	1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs1415072	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs1884447	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs2050566	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2057222	0.81[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap]
rs2146328	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2146329	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2378958	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs3753569	1.00[CEU][hapmap]
rs3766720	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs3766723	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6674490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs6698122	0.91[JPT][hapmap]
rs6700484	1.00[CEU][hapmap]
rs7519019	0.84[GIH][hapmap]
rs7523448	0.84[TSI][hapmap]
rs7548237	0.84[TSI][hapmap]
rs950327	0.84[TSI][hapmap]

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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS 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 target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv872588	chr1:185081903-185117688	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548397	chr1:185104842-185123630	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6684586	QSOX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:185073600-185115000	Weak transcription	NH-A	brain
4	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
5	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
6	chr1:185085000-185121400	Weak transcription	NHEK	skin
7	chr1:185085400-185125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:185086000-185120200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:185087000-185125000	Weak transcription	Gastric	stomach
10	chr1:185087600-185117000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:185088200-185120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:185089400-185124400	Weak transcription	Colonic Mucosa	Colon
13	chr1:185089600-185121400	Weak transcription	Stomach Mucosa	stomach
14	chr1:185091200-185121400	Weak transcription	Fetal Heart	heart
15	chr1:185093800-185117400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:185094200-185116600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:185094200-185118400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:185096600-185121400	Weak transcription	Hela-S3	cervix
19	chr1:185101000-185121000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:185101600-185125200	Weak transcription	Esophagus	oesophagus
21	chr1:185101800-185120200	Strong transcription	Adipose Nuclei	Adipose
22	chr1:185101800-185120800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:185102000-185120800	Strong transcription	Placenta	Placenta
24	chr1:185102400-185120600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:185102400-185121400	Weak transcription	HMEC	breast
26	chr1:185102400-185124400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:185102600-185124400	Weak transcription	Fetal Brain Male	brain
28	chr1:185102600-185124400	Weak transcription	Small Intestine	intestine
29	chr1:185102800-185117400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:185102800-185121200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:185102800-185125000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:185103000-185116600	Weak transcription	Fetal Brain Female	brain
33	chr1:185103000-185121400	Weak transcription	Aorta	Aorta
34	chr1:185103000-185124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:185103200-185117400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:185103200-185121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:185103200-185121000	Weak transcription	HSMMtube	muscle
38	chr1:185103400-185123600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:185103600-185123800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:185103600-185124400	Weak transcription	Brain Substantia Nigra	brain
41	chr1:185104200-185123000	Weak transcription	HepG2	liver
42	chr1:185104600-185116600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:185104600-185125000	Weak transcription	Pancreas	Pancrea
44	chr1:185104800-185116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:185105200-185120400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:185105600-185118400	Weak transcription	Thymus	Thymus
47	chr1:185105600-185125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:185105600-185125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:185105600-185125200	Weak transcription	Lung	lung
50	chr1:185106000-185124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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