Variant report

Variant	rs6424971
Chromosome Location	chr1:185110367-185110368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185110219..185112548-chr1:185124480..185127523,3	MCF-7	breast:
2	chr1:185097360..185099907-chr1:185110020..185112748,3	K562	blood:

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1046592	0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs10489580	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs10737256	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10752945	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10797998	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs10797999	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10798000	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs10911678	0.95[ASN][1000 genomes]
rs10911680	0.99[ASN][1000 genomes]
rs11588646	0.99[ASN][1000 genomes]
rs12025737	0.95[ASN][1000 genomes]
rs12030554	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12081098	0.88[ASN][1000 genomes]
rs12086086	0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs12404187	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12404644	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs12566975	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322646	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1407555	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1407556	0.98[ASN][1000 genomes]
rs1407557	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1544052	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1884447	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2057222	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2146329	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3753569	0.99[ASN][1000 genomes]
rs4549995	0.99[ASN][1000 genomes]
rs6424972	0.83[CHD][hapmap]
rs6660169	0.81[CHD][hapmap]
rs6673303	0.81[CHD][hapmap]
rs6700484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7512290	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7519019	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7533198	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7547420	0.89[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	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
rs6424971	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	chr1:185093800-185113400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:185093800-185117400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:185094000-185110800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:185094000-185113000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:185094200-185116600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:185094200-185118400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:185096600-185121400	Weak transcription	Hela-S3	cervix
22	chr1:185100000-185110800	Weak transcription	NHLF	lung
23	chr1:185100800-185111200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:185101000-185121000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:185101600-185125200	Weak transcription	Esophagus	oesophagus
26	chr1:185101800-185120200	Strong transcription	Adipose Nuclei	Adipose
27	chr1:185101800-185120800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:185102000-185120800	Strong transcription	Placenta	Placenta
29	chr1:185102400-185110600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:185102400-185113400	Weak transcription	HUVEC	blood vessel
31	chr1:185102400-185120600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:185102400-185121400	Weak transcription	HMEC	breast
33	chr1:185102400-185124400	Weak transcription	Brain Germinal Matrix	brain
34	chr1:185102600-185124400	Weak transcription	Fetal Brain Male	brain
35	chr1:185102600-185124400	Weak transcription	Small Intestine	intestine
36	chr1:185102800-185111800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:185102800-185112400	Weak transcription	Dnd41	blood
38	chr1:185102800-185117400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:185102800-185121200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:185102800-185125000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:185103000-185110600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:185103000-185113600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:185103000-185116600	Weak transcription	Fetal Brain Female	brain
44	chr1:185103000-185121400	Weak transcription	Aorta	Aorta
45	chr1:185103000-185124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:185103200-185113200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:185103200-185117400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:185103200-185121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:185103200-185121000	Weak transcription	HSMMtube	muscle
50	chr1:185103400-185112200	Weak transcription	NHDF-Ad	bronchial

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