Variant report

Variant	rs2296029
Chromosome Location	chr13:52335765-52335766
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	chr13:52312271..52315134-chr13:52333689..52336005,2	K562	blood:

Variant related genes	Relation type
ENSG00000139668	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1060562	0.99[ASN][1000 genomes]
rs12146894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1475195	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17532412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17597531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1885854	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2031993	1.00[MKK][hapmap]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2897944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555048	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	1.00[AFR][1000 genomes]
rs488261	1.00[AFR][1000 genomes]
rs60757273	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73199734	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9526793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9535722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9535734	0.91[ASN][1000 genomes]
rs9535735	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535738	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535746	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2296029	WDFY2	cis	parietal	SCAN
rs2296029	HNRNPA1L2	cis	parietal	SCAN
rs2296029	CKAP2	cis	parietal	SCAN
rs2296029	WDFY2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
3	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:52322600-52337000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:52322600-52338200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:52322600-52338200	Weak transcription	Stomach Mucosa	stomach
7	chr13:52322600-52342200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:52322600-52342200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr13:52322800-52337600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:52322800-52338200	Weak transcription	HUVEC	blood vessel
11	chr13:52323000-52336400	Weak transcription	K562	blood
12	chr13:52323000-52336600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr13:52323000-52337200	Strong transcription	Primary B cells from cord blood	blood
14	chr13:52323000-52343400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr13:52323200-52336800	Strong transcription	Primary hematopoietic stem cells	blood
16	chr13:52323200-52337600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr13:52323200-52338200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr13:52323200-52341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:52324400-52335800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr13:52324400-52337000	Strong transcription	HepG2	liver
21	chr13:52324400-52337200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr13:52324600-52336600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr13:52324600-52336800	Strong transcription	Primary T cells from cord blood	blood
24	chr13:52324600-52337400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:52324800-52336800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:52324800-52337600	Strong transcription	Liver	Liver
27	chr13:52324800-52338200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr13:52324800-52342600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr13:52325400-52337800	Strong transcription	Thymus	Thymus
30	chr13:52325400-52338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr13:52325600-52337600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr13:52326000-52342600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr13:52326400-52336000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr13:52326600-52335800	Strong transcription	Osteobl	bone
35	chr13:52326600-52337000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr13:52327000-52337400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:52327600-52343200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:52327800-52337600	Strong transcription	NHEK	skin
39	chr13:52327800-52343000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:52328400-52336800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:52329000-52336600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:52329000-52337200	Strong transcription	Fetal Stomach	stomach
43	chr13:52329200-52337000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:52329400-52336000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr13:52329600-52336800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr13:52329600-52338200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr13:52330400-52336600	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr13:52330400-52341800	Weak transcription	Hela-S3	cervix
49	chr13:52330600-52338200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr13:52330600-52339000	Weak transcription	Colon Smooth Muscle	Colon

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