Variant report

Variant	rs9535739
Chromosome Location	chr13:52283300-52283301
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	chr13:52282244..52284170-chr13:52327994..52329848,2	K562	blood:
2	chr13:52025091..52028309-chr13:52280990..52283618,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1060562	0.96[ASN][1000 genomes]
rs12146894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1475195	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17532412	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[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17597531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1885854	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];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296029	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]
rs2780461	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs2897944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4555048	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs491103	0.86[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs60757273	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73199734	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526786	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535722	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535734	0.96[ASN][1000 genomes]
rs9535735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535738	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535744	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[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535746	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];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535739	HNRNPA1L2	cis	parietal	SCAN
rs9535739	WDFY2	cis	cerebellum	SCAN
rs9535739	CKAP2	cis	parietal	SCAN
rs9535739	WDFY2	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52247600-52300200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:52247600-52300200	Weak transcription	Fetal Lung	lung
3	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:52254600-52293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:52263400-52295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr13:52264000-52300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:52270400-52293200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:52272200-52288800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:52272400-52287600	Weak transcription	NHDF-Ad	bronchial
13	chr13:52272400-52288800	Weak transcription	NHLF	lung
14	chr13:52273400-52291800	Weak transcription	Brain Anterior Caudate	brain
15	chr13:52273600-52291400	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:52273600-52293000	Weak transcription	Right Atrium	heart
17	chr13:52273600-52293200	Weak transcription	Left Ventricle	heart
18	chr13:52273600-52295200	Weak transcription	Right Ventricle	heart
19	chr13:52273600-52295600	Weak transcription	Pancreas	Pancrea
20	chr13:52273600-52295800	Weak transcription	Spleen	Spleen
21	chr13:52274000-52295600	Weak transcription	Ovary	ovary
22	chr13:52274000-52300400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:52275200-52284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr13:52276400-52285000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:52276400-52295400	Weak transcription	Adipose Nuclei	Adipose
26	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:52276800-52288800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr13:52277000-52283600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:52277000-52300000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr13:52277800-52283600	Strong transcription	HSMM	muscle
31	chr13:52278000-52287200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr13:52278400-52299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr13:52278800-52301800	Weak transcription	Thymus	Thymus
34	chr13:52278800-52302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr13:52279200-52288000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:52279400-52287600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:52279400-52291800	Weak transcription	Aorta	Aorta
38	chr13:52279400-52295200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr13:52279400-52300200	Weak transcription	Liver	Liver
40	chr13:52279400-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:52279400-52301800	Weak transcription	Gastric	stomach
42	chr13:52279400-52303000	Weak transcription	Lung	lung
43	chr13:52279600-52287400	Weak transcription	NHEK	skin
44	chr13:52279600-52287600	Weak transcription	HMEC	breast
45	chr13:52279600-52288600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr13:52279600-52288800	Weak transcription	NH-A	brain
47	chr13:52279600-52293000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr13:52279600-52293200	Weak transcription	Primary T cells from cord blood	blood
49	chr13:52279600-52295000	Weak transcription	HSMMtube	muscle
50	chr13:52279600-52299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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