Variant report

Variant	rs28609768
Chromosome Location	chr1:185033480-185033481
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185032736..185034530-chr1:185034703..185036671,2	K562	blood:
2	chr1:185015280..185017121-chr1:185031346..185033713,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1053166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs10911679	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.93[EUR][1000 genomes]
rs12119759	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12385701	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12408074	0.86[AMR][1000 genomes]
rs12563135	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12566404	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2378957	0.88[ASW][hapmap];0.90[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34916432	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34969721	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3820183	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6674490	0.81[TSI][hapmap]
rs6677056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6699626	0.86[EUR][1000 genomes]
rs7523448	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7548237	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs950327	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv525731	chr1:184812165-185038104	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28609768	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185015600-185034200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:185015600-185037000	Weak transcription	Spleen	Spleen
3	chr1:185015600-185037600	Weak transcription	Pancreas	Pancrea
4	chr1:185015800-185037600	Weak transcription	Aorta	Aorta
5	chr1:185015800-185043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:185016000-185034400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:185016400-185057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:185016400-185067200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:185016400-185073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:185016600-185057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:185017200-185037400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:185017400-185037200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:185017400-185037400	Weak transcription	NHEK	skin
14	chr1:185017400-185042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:185017600-185034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:185018400-185043000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:185018400-185043200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
19	chr1:185019000-185034600	Weak transcription	Lung	lung
20	chr1:185019200-185037600	Weak transcription	Left Ventricle	heart
21	chr1:185020400-185039000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:185020600-185040200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:185021600-185057200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:185024200-185044000	Weak transcription	Fetal Stomach	stomach
25	chr1:185024200-185056600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:185027200-185056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:185027200-185056400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:185027400-185034600	Weak transcription	Ovary	ovary
29	chr1:185027400-185038000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:185027400-185040000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:185027600-185039000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:185028200-185035200	Weak transcription	Fetal Lung	lung
33	chr1:185028200-185037600	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:185028200-185039400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:185028200-185058200	Weak transcription	Brain Substantia Nigra	brain
36	chr1:185028600-185033600	Weak transcription	A549	lung
37	chr1:185028800-185038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:185028800-185043400	Weak transcription	Small Intestine	intestine
39	chr1:185029200-185035200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:185029200-185037600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:185029600-185042600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:185030200-185041200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:185030200-185076600	Weak transcription	Gastric	stomach
44	chr1:185031000-185035400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:185031000-185037600	Weak transcription	Primary T cells from cord blood	blood
46	chr1:185031200-185035200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:185031200-185037400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:185031200-185044000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:185031200-185044400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:185031400-185034600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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