Variant report

Variant	rs3803201
Chromosome Location	chr13:52293509-52293510
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	chr13:52023064..52027990-chr13:52292653..52297533,6	MCF-7	breast:
2	chr13:52162012..52164876-chr13:52292146..52294870,2	K562	blood:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1024271	0.95[JPT][hapmap]
rs12585249	0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs17075902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[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]
rs3825410	1.00[ASW][hapmap];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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075628	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4625625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4941703	0.85[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs4941710	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943005	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs4943009	0.94[GIH][hapmap]
rs4943018	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328695	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7333623	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs745374	1.00[ASW][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[AFR][1000 genomes]
rs7986066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316547	0.90[JPT][hapmap]
rs9316551	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs9563061	1.00[ASW][hapmap]
rs9563063	0.85[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs9563065	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9563066	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9563067	1.00[ASW][hapmap];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[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568644	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9568647	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568649	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568653	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568658	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9805172	0.85[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3803201	WDFY2	cis	parietal	SCAN
rs3803201	NCRNA00282	cis	parietal	SCAN
rs3803201	MANF	trans	parietal	SCAN
rs3803201	TRIM13	cis	cerebellum	SCAN

Chromatin state (count:93 , 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	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:52263400-52295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:52264000-52300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr13:52273600-52295200	Weak transcription	Right Ventricle	heart
10	chr13:52273600-52295600	Weak transcription	Pancreas	Pancrea
11	chr13:52273600-52295800	Weak transcription	Spleen	Spleen
12	chr13:52274000-52295600	Weak transcription	Ovary	ovary
13	chr13:52274000-52300400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:52276400-52295400	Weak transcription	Adipose Nuclei	Adipose
15	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:52277000-52300000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr13:52278400-52299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr13:52278800-52301800	Weak transcription	Thymus	Thymus
19	chr13:52278800-52302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:52279400-52295200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr13:52279400-52300200	Weak transcription	Liver	Liver
22	chr13:52279400-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:52279400-52301800	Weak transcription	Gastric	stomach
24	chr13:52279400-52303000	Weak transcription	Lung	lung
25	chr13:52279600-52295000	Weak transcription	HSMMtube	muscle
26	chr13:52279600-52299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:52279600-52300000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr13:52279600-52301800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:52279600-52301800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr13:52279600-52304000	Weak transcription	Esophagus	oesophagus
31	chr13:52280200-52301600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr13:52281000-52294800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:52282000-52302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:52283600-52297200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:52284800-52301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr13:52287800-52295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr13:52288400-52322200	Weak transcription	K562	blood
38	chr13:52288600-52303000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr13:52289000-52300200	Weak transcription	Hela-S3	cervix
40	chr13:52289000-52301800	Weak transcription	A549	lung
41	chr13:52289200-52293600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:52289200-52300000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr13:52289400-52305800	Weak transcription	Fetal Kidney	kidney
44	chr13:52290000-52300400	Weak transcription	NH-A	brain
45	chr13:52290000-52307600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr13:52290200-52301600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:52290400-52293600	Weak transcription	HMEC	breast
48	chr13:52291400-52293600	Enhancers	Brain Hippocampus Middle	brain
49	chr13:52291400-52295400	Strong transcription	HepG2	liver
50	chr13:52291400-52297200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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