Variant report

Variant	rs2146329
Chromosome Location	chr1:185132842-185132843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185014319..185017930-chr1:185131535..185134383,3	K562	blood:
2	chr1:185126593..185129222-chr1:185131770..185134978,3	K562	blood:
3	chr1:185013840..185015819-chr1:185132627..185134383,2	K562	blood:
4	chr1:185126236..185129657-chr1:185130448..185133480,5	K562	blood:

Variant related genes	Relation type
ENSG00000121481	Chromatin interaction
ENSG00000116668	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1046592	0.86[CHB][hapmap]
rs10489580	0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1053166	0.82[TSI][hapmap]
rs10737256	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10752945	0.84[ASN][1000 genomes]
rs10797998	0.86[CHB][hapmap]
rs10797999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798000	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.83[MKK][hapmap]
rs10911678	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911679	0.82[TSI][hapmap]
rs10911680	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11588646	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12025737	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12030554	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12081098	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12086086	0.86[CHB][hapmap]
rs12404187	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12404644	0.86[CHB][hapmap]
rs12566975	0.92[ASN][1000 genomes]
rs1322646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407555	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1407556	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407557	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1544052	0.86[CHB][hapmap]
rs1591585	0.82[CHB][hapmap]
rs1884447	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]
rs2057222	0.90[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3753569	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4549995	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6424971	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6424972	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs6660169	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs6673303	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs6674490	0.90[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6684586	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs6700484	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7512290	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7519019	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7523448	0.84[TSI][hapmap]
rs7533198	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7547420	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7548237	0.84[TSI][hapmap]
rs950327	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2146329	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127200-185147000	Weak transcription	Spleen	Spleen
2	chr1:185127200-185169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:185127400-185133400	Weak transcription	Lung	lung
4	chr1:185127400-185135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:185127400-185135600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:185127400-185136400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:185127400-185144400	Weak transcription	Pancreas	Pancrea
8	chr1:185127400-185152200	Weak transcription	Aorta	Aorta
9	chr1:185127400-185153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:185127400-185157400	Weak transcription	Small Intestine	intestine
11	chr1:185127400-185163400	Weak transcription	Esophagus	oesophagus
12	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:185127600-185133200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:185127600-185133600	Weak transcription	Primary B cells from cord blood	blood
15	chr1:185127600-185134200	Weak transcription	Ovary	ovary
16	chr1:185127600-185135200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:185127600-185135800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:185127600-185136400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:185127600-185138400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:185127600-185138800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:185127600-185139200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:185127600-185139400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:185127600-185139400	Weak transcription	Fetal Kidney	kidney
24	chr1:185127600-185144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:185127600-185144800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:185127600-185145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:185127600-185145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:185127600-185147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:185127600-185170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
31	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
32	chr1:185127800-185134000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:185127800-185136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:185127800-185147000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:185128000-185135600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:185128000-185136200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:185128000-185136600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:185128000-185137000	Weak transcription	NH-A	brain
39	chr1:185128000-185166400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:185128200-185133600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:185128200-185133600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:185128200-185133800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:185128200-185133800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:185128200-185134000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:185128200-185134000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:185128200-185135000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:185128200-185135000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:185128200-185135200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:185128200-185135800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:185128200-185139400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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