Variant report

Variant	rs17075902
Chromosome Location	chr13:52296067-52296068
allele	G/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	chr13:52025496..52027333-chr13:52294582..52296334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1024271	0.95[JPT][hapmap]
rs12585249	0.89[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs3803201	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];0.94[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];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[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];1.00[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];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs4943009	0.89[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];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[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]
rs9563063	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[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];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[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];1.00[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
rs17075902	MANF	trans	parietal	SCAN
rs17075902	WDFY2	cis	parietal	SCAN
rs17075902	TRIM13	cis	cerebellum	SCAN
rs17075902	NCRNA00282	cis	parietal	SCAN

Chromatin state (count:100 , 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	chr13:52264000-52300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr13:52274000-52300400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr13:52277000-52300000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr13:52278400-52299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr13:52278800-52301800	Weak transcription	Thymus	Thymus
13	chr13:52278800-52302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:52279400-52300200	Weak transcription	Liver	Liver
15	chr13:52279400-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:52279400-52301800	Weak transcription	Gastric	stomach
17	chr13:52279400-52303000	Weak transcription	Lung	lung
18	chr13:52279600-52299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:52279600-52300000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr13:52279600-52301800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr13:52279600-52301800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr13:52279600-52304000	Weak transcription	Esophagus	oesophagus
23	chr13:52280200-52301600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr13:52282000-52302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr13:52283600-52297200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:52284800-52301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:52288400-52322200	Weak transcription	K562	blood
28	chr13:52288600-52303000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr13:52289000-52300200	Weak transcription	Hela-S3	cervix
30	chr13:52289000-52301800	Weak transcription	A549	lung
31	chr13:52289200-52300000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr13:52289400-52305800	Weak transcription	Fetal Kidney	kidney
33	chr13:52290000-52300400	Weak transcription	NH-A	brain
34	chr13:52290000-52307600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr13:52290200-52301600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:52291400-52297200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:52291400-52303000	Weak transcription	Fetal Stomach	stomach
38	chr13:52291600-52296400	Enhancers	Brain Substantia Nigra	brain
39	chr13:52292200-52298200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr13:52292200-52301800	Weak transcription	Dnd41	blood
41	chr13:52292200-52302600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr13:52292200-52304400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr13:52292400-52300600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:52292400-52304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr13:52292600-52300200	Weak transcription	NHDF-Ad	bronchial
46	chr13:52292800-52300400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr13:52293000-52296400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:52293200-52296400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:52293200-52298000	Strong transcription	HSMM	muscle
50	chr13:52293200-52303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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