Variant report

Variant	rs1884447
Chromosome Location	chr1:185021410-185021411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185016452..185019529-chr1:185020434..185022223,3	MCF-7	breast:
2	chr1:185020834..185023739-chr1:185029280..185032218,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1046592	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs10489580	0.86[JPT][hapmap]
rs10737256	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10752945	0.89[ASN][1000 genomes]
rs10797998	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10797999	0.90[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798000	0.81[JPT][hapmap]
rs10911678	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911680	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11588646	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12025737	0.93[ASN][1000 genomes]
rs12030554	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12081098	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12086086	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs12404187	0.81[JPT][hapmap]
rs12404644	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs12566975	0.91[ASN][1000 genomes]
rs1322646	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407555	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1407556	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1407557	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1544052	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2057222	0.81[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.94[YRI][hapmap];0.94[ASN][1000 genomes]
rs2146329	0.90[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3753569	0.96[CEU][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4549995	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6424971	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6674490	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs6684586	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs6700484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512290	0.81[JPT][hapmap]
rs7519019	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.99[ASN][1000 genomes]
rs7533198	0.81[JPT][hapmap]
rs7547420	0.90[EUR][1000 genomes];0.91[ASN][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
rs1884447	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:78 , 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	chr1:185015800-185023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:185015800-185037600	Weak transcription	Aorta	Aorta
6	chr1:185015800-185043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:185016000-185025600	Weak transcription	Ovary	ovary
8	chr1:185016000-185026600	Weak transcription	Psoas Muscle	Psoas
9	chr1:185016000-185026600	Weak transcription	Right Atrium	heart
10	chr1:185016000-185034400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:185016200-185023600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:185016400-185022600	Weak transcription	Placenta	Placenta
13	chr1:185016400-185030000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:185016400-185057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:185016400-185067200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:185016400-185073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:185016600-185022600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:185016600-185026600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:185016600-185026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:185016600-185026800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:185016600-185057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:185016800-185028600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:185017200-185027400	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:185017200-185037400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:185017400-185021800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:185017400-185023400	Weak transcription	Fetal Intestine Large	intestine
27	chr1:185017400-185026600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:185017400-185026600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:185017400-185026600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:185017400-185026800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:185017400-185027600	Weak transcription	Primary T cells from cord blood	blood
32	chr1:185017400-185028200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:185017400-185028200	Weak transcription	Small Intestine	intestine
34	chr1:185017400-185028400	Weak transcription	NH-A	brain
35	chr1:185017400-185029000	Weak transcription	K562	blood
36	chr1:185017400-185031000	Weak transcription	Stomach Mucosa	stomach
37	chr1:185017400-185037200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:185017400-185037400	Weak transcription	NHEK	skin
39	chr1:185017400-185042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:185017600-185022400	Weak transcription	Dnd41	blood
41	chr1:185017600-185034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:185017800-185026600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:185018000-185026600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:185018000-185026600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:185018000-185026800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:185018000-185026800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:185018200-185026600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:185018400-185043000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:185018400-185043200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain

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