Variant report

Variant	rs17069413
Chromosome Location	chr13:52210268-52210269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52025930..52028470-chr13:52210026..52212649,2	K562	blood:
2	chr13:52025659..52027430-chr13:52210026..52212252,2	K562	blood:

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

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1058141	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs1058142	0.93[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs10676	0.88[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes]
rs12146894	0.86[ASW][hapmap];0.81[MKK][hapmap]
rs12427805	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12428478	0.85[CEU][hapmap];0.96[GIH][hapmap];0.88[AMR][1000 genomes]
rs12430600	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12430760	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12431173	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17075849	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17531181	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2011276	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2296027	0.85[CEU][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes]
rs2408491	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2897944	0.81[ASW][hapmap]
rs4399447	0.83[AMR][1000 genomes]
rs55910561	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs57280031	0.82[AMR][1000 genomes]
rs57837262	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs59291282	0.96[AMR][1000 genomes]
rs73199739	0.88[AMR][1000 genomes]
rs73199742	0.89[AMR][1000 genomes]
rs73199750	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7321346	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7329391	0.93[ASW][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[AMR][1000 genomes]
rs74086223	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7985214	0.87[AMR][1000 genomes]
rs8001480	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9526795	0.93[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs9535754	0.86[ASW][hapmap];0.93[LWK][hapmap];0.81[AFR][1000 genomes]
rs9568662	0.89[YRI][hapmap];0.93[AMR][1000 genomes]
rs9596530	0.85[CEU][hapmap]
rs9596572	0.85[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes]
rs9596573	0.87[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17069413	FLJ13639	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52194800-52217600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:52197600-52212400	Weak transcription	Fetal Kidney	kidney
3	chr13:52198600-52217600	Weak transcription	Fetal Thymus	thymus
4	chr13:52201200-52210800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr13:52202600-52210400	Weak transcription	Right Atrium	heart
6	chr13:52202800-52217600	Weak transcription	Fetal Stomach	stomach
7	chr13:52203000-52210800	Weak transcription	Right Ventricle	heart
8	chr13:52203000-52213600	Weak transcription	Colon Smooth Muscle	Colon
9	chr13:52205200-52212200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:52205200-52214600	Enhancers	Brain Substantia Nigra	brain
11	chr13:52207200-52212400	Weak transcription	Hela-S3	cervix
12	chr13:52207200-52212600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr13:52207200-52218400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:52207400-52210400	Weak transcription	Ovary	ovary
15	chr13:52207400-52210600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:52207400-52211200	Weak transcription	NHLF	lung
17	chr13:52207400-52212000	Weak transcription	Esophagus	oesophagus
18	chr13:52207600-52210400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr13:52207600-52210400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:52207600-52210400	Weak transcription	Fetal Lung	lung
21	chr13:52207600-52210600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr13:52207600-52210800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:52207600-52211200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:52207600-52211200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr13:52207600-52212000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:52207600-52212200	Weak transcription	HSMMtube	muscle
27	chr13:52207600-52214600	Enhancers	Brain Cingulate Gyrus	brain
28	chr13:52207600-52217000	Weak transcription	Adipose Nuclei	Adipose
29	chr13:52207600-52220200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:52207800-52210400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr13:52207800-52210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:52207800-52210400	Weak transcription	HSMM	muscle
33	chr13:52207800-52210400	Weak transcription	NH-A	brain
34	chr13:52207800-52210400	Weak transcription	NHDF-Ad	bronchial
35	chr13:52207800-52210600	Weak transcription	Aorta	Aorta
36	chr13:52207800-52211600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:52207800-52214600	Enhancers	Brain Hippocampus Middle	brain
38	chr13:52207800-52217400	Weak transcription	Brain Germinal Matrix	brain
39	chr13:52208000-52210800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:52208000-52210800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:52208200-52210400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr13:52208200-52220000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:52208400-52210400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:52208600-52210400	Weak transcription	Osteobl	bone
45	chr13:52208800-52210600	Enhancers	Primary B cells from peripheral blood	blood
46	chr13:52208800-52211000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr13:52209000-52210400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr13:52209200-52210400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr13:52209200-52210600	Enhancers	Primary B cells from cord blood	blood
50	chr13:52209200-52212000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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