Variant report

Variant	rs9535744
Chromosome Location	chr13:52311481-52311482
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr13:52311447-52311506	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52158067..52160391-chr13:52310878..52313394,2	MCF-7	breast:

Variant related genes	Relation type
WDFY2	TF binding region
ENSG00000139668	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1024271	1.00[YRI][hapmap]
rs1060562	1.00[ASN][1000 genomes]
rs12146894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12585249	1.00[YRI][hapmap]
rs1475195	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17075907	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532524	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532936	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17597215	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17597531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1885854	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296029	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]
rs2780461	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2897944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3908968	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41292776	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4555048	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap]
rs4943005	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs60757273	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73199734	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73199746	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526786	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526788	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9526793	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[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526794	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535717	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9535722	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9535734	0.92[ASN][1000 genomes]
rs9535735	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535737	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535738	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535739	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]
rs9535741	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535743	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535745	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535746	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535751	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535752	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535755	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9563063	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9535744	HNRNPA1L2	cis	parietal	SCAN
rs9535744	CKAP2	cis	parietal	SCAN
rs9535744	WDFY2	cis	parietal	SCAN
rs9535744	FLJ13639	cis	multi-tissue	Pritchard
rs9535744	WDFY2	cis	cerebellum	SCAN
rs9535744	WDFY2	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52288400-52322200	Weak transcription	K562	blood
2	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
3	chr13:52297000-52311800	Weak transcription	GM12878-XiMat	blood
4	chr13:52298000-52322200	Weak transcription	Fetal Brain Female	brain
5	chr13:52300200-52311800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:52300400-52322200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr13:52300600-52316000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr13:52300600-52321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:52302200-52314000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:52302400-52313000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:52302600-52313800	Weak transcription	Dnd41	blood
12	chr13:52302800-52313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr13:52302800-52313200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr13:52303400-52315000	Weak transcription	Fetal Thymus	thymus
15	chr13:52303800-52313600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr13:52304000-52320400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:52305000-52311800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:52305000-52313000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:52305000-52313200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:52305000-52313200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:52305000-52320400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr13:52305200-52313200	Weak transcription	Placenta	Placenta
24	chr13:52305200-52320400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:52305400-52311800	Weak transcription	Esophagus	oesophagus
26	chr13:52305400-52313800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr13:52305400-52315000	Weak transcription	Fetal Stomach	stomach
28	chr13:52305400-52321600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:52305400-52321800	Weak transcription	Gastric	stomach
30	chr13:52305600-52314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr13:52305800-52313000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:52305800-52322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:52306000-52313000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr13:52306000-52313200	Weak transcription	Fetal Lung	lung
35	chr13:52306000-52313200	Weak transcription	Pancreas	Pancrea
36	chr13:52306000-52314200	Weak transcription	NHLF	lung
37	chr13:52306000-52317800	Weak transcription	Small Intestine	intestine
38	chr13:52306000-52322200	Weak transcription	Left Ventricle	heart
39	chr13:52306000-52322200	Weak transcription	Right Ventricle	heart
40	chr13:52306200-52313000	Weak transcription	Colon Smooth Muscle	Colon
41	chr13:52306200-52313200	Weak transcription	Brain Germinal Matrix	brain
42	chr13:52306200-52321400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
44	chr13:52306400-52312800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:52306400-52313000	Weak transcription	NHDF-Ad	bronchial
46	chr13:52306400-52320400	Weak transcription	Aorta	Aorta
47	chr13:52306600-52313200	Weak transcription	Ovary	ovary
48	chr13:52307800-52312000	Strong transcription	Primary B cells from cord blood	blood
49	chr13:52307800-52313000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:52307800-52313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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