Variant report

Variant	rs6677056
Chromosome Location	chr1:185054687-185054688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185054642..185056365-chr1:185060219..185062027,2	K562	blood:
2	chr1:185052742..185055562-chr1:185064799..185067162,2	MCF-7	breast:
3	chr1:185052198..185055026-chr1:185055673..185057195,2	K562	blood:

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];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10911679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs12119759	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12385701	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12408074	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12563135	0.91[AMR][1000 genomes]
rs12566404	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2378957	0.90[GIH][hapmap];0.86[ASN][1000 genomes]
rs28609768	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]
rs34463352	0.92[AFR][1000 genomes]
rs34916432	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34969721	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3820183	0.88[ASN][1000 genomes]
rs6699626	0.85[EUR][1000 genomes]
rs7523448	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7548237	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs950327	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6677056	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185016400-185057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:185016400-185067200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:185016400-185073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:185016600-185057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
6	chr1:185021600-185057200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:185024200-185056600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:185027200-185056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:185027200-185056400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:185028200-185058200	Weak transcription	Brain Substantia Nigra	brain
11	chr1:185030200-185076600	Weak transcription	Gastric	stomach
12	chr1:185032200-185057800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:185032800-185056600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:185034800-185057400	Weak transcription	Fetal Brain Female	brain
15	chr1:185034800-185077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:185035000-185056600	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:185035000-185058000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:185035200-185056600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:185035400-185057000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:185035800-185056400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:185035800-185057800	Weak transcription	Fetal Lung	lung
22	chr1:185036000-185056600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:185036000-185056600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:185037400-185056800	Weak transcription	Placenta	Placenta
25	chr1:185037800-185056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:185037800-185056800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:185037800-185065400	Weak transcription	HMEC	breast
28	chr1:185038400-185063600	Weak transcription	Psoas Muscle	Psoas
29	chr1:185038600-185063600	Weak transcription	Left Ventricle	heart
30	chr1:185041000-185056400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:185041200-185056400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:185041200-185056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:185041600-185056600	Weak transcription	Primary B cells from cord blood	blood
34	chr1:185043200-185055600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:185043600-185056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:185043600-185069400	Weak transcription	Pancreas	Pancrea
37	chr1:185044000-185065200	Weak transcription	NHEK	skin
38	chr1:185044400-185057400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:185044800-185056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:185044800-185056600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:185044800-185056800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:185044800-185057000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:185044800-185057600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:185045000-185068800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:185045400-185055200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:185046000-185066000	Weak transcription	Stomach Mucosa	stomach
47	chr1:185046200-185055200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:185046400-185055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:185047800-185055200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:185048600-185056600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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