Variant report

Variant	rs9535722
Chromosome Location	chr13:52207488-52207489
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52025536..52027203-chr13:52206124..52208058,2	MCF-7	breast:
2	chr13:52022346..52024243-chr13:52205335..52207753,2	MCF-7	breast:
3	chr13:52025159..52027320-chr13:52206215..52208179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12146894	1.00[JPT][hapmap]
rs12427748	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1475195	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17532412	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17597531	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];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1885854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes]
rs2296029	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]
rs2780461	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2897944	1.00[JPT][hapmap]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4555048	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];0.86[ASN][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs491103	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap];0.83[GIH][hapmap]
rs60757273	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6561638	1.00[ASW][hapmap];0.85[GIH][hapmap]
rs73199734	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526786	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];0.86[ASN][1000 genomes]
rs9526788	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];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526793	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];0.83[EUR][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535699	1.00[ASW][hapmap]
rs9535714	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535735	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535738	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535739	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]
rs9535741	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9535744	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535748	1.00[JPT][hapmap]
rs9535749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535756	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][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
rs9535722	WDFY2	cis	parietal	SCAN
rs9535722	HNRNPA1L2	cis	parietal	SCAN
rs9535722	CKAP2	cis	parietal	SCAN
rs9535722	WDFY2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52189400-52208800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr13:52194200-52209400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:52194800-52217600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:52197600-52212400	Weak transcription	Fetal Kidney	kidney
5	chr13:52198000-52209400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:52198600-52217600	Weak transcription	Fetal Thymus	thymus
7	chr13:52200600-52209400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:52201200-52210800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:52202600-52209400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:52202600-52210400	Weak transcription	Right Atrium	heart
11	chr13:52202800-52217600	Weak transcription	Fetal Stomach	stomach
12	chr13:52203000-52210800	Weak transcription	Right Ventricle	heart
13	chr13:52203000-52213600	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:52203400-52209600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:52204200-52207800	Enhancers	NHEK	skin
16	chr13:52204400-52208800	Weak transcription	Primary T cells from cord blood	blood
17	chr13:52204400-52209400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr13:52205200-52212200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr13:52205200-52214600	Enhancers	Brain Substantia Nigra	brain
20	chr13:52205400-52207800	Enhancers	NHDF-Ad	bronchial
21	chr13:52205400-52208600	Enhancers	Brain Anterior Caudate	brain
22	chr13:52205600-52207800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:52205600-52207800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:52205600-52207800	Enhancers	NH-A	brain
25	chr13:52205600-52208000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:52205800-52207800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr13:52205800-52208000	Enhancers	Brain Angular Gyrus	brain
28	chr13:52206000-52207600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:52206000-52207600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr13:52206000-52208400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr13:52206000-52209200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr13:52206200-52207600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr13:52206200-52208200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr13:52206400-52207600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr13:52206400-52207600	Enhancers	GM12878-XiMat	blood
36	chr13:52206400-52207800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr13:52206600-52207600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:52206600-52207600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr13:52206600-52207600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:52206600-52207600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:52206600-52207600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:52206600-52207800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr13:52206600-52207800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr13:52206600-52207800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:52206600-52207800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr13:52206600-52207800	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr13:52206600-52208600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:52206800-52207600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr13:52206800-52207600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr13:52206800-52207600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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