Variant report

Variant	rs17319759
Chromosome Location	chr10:5962890-5962891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5855163..5856698-chr10:5960274..5962988,2	MCF-7	breast:
2	chr10:5951474..5953291-chr10:5960290..5963166,2	K562	blood:
3	chr10:5957022..5959868-chr10:5961811..5965784,4	K562	blood:
4	chr10:5957299..5960172-chr10:5961811..5965784,4	K562	blood:

Variant related genes	Relation type
ENSG00000272764	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10508298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255698	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255774	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255780	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255971	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256009	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12360409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12767690	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774228	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12781700	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976655	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985072	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387092	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049919	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891620	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs56369297	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832959	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919913	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1041261	chr10:5962635-6052196	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17319759	ANKRD16	cis	parietal	SCAN
rs17319759	ANKRD16	cis	cerebellum	SCAN
rs17319759	IL15RA	cis	parietal	SCAN
rs17319759	AKR1C2	cis	cerebellum	SCAN
rs17319759	AKR1C3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
3	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
4	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
5	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
7	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
8	chr10:5947400-5970800	Strong transcription	Liver	Liver
9	chr10:5947400-5974400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:5947600-5968400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:5947600-5968600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:5947600-5968600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr10:5947600-5975000	Strong transcription	Primary T cells from cord blood	blood
15	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr10:5947800-5974000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:5947800-5974400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:5947800-5974600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr10:5948000-5974600	Strong transcription	Fetal Lung	lung
24	chr10:5948000-5974800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:5948000-5975000	Strong transcription	Primary B cells from cord blood	blood
26	chr10:5948000-5975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:5948200-5974000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr10:5948200-5974800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr10:5948800-5974200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr10:5949400-5970200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr10:5949600-5975600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr10:5949800-5967200	Strong transcription	Adipose Nuclei	Adipose
39	chr10:5949800-5973400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr10:5949800-5975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr10:5950000-5976400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr10:5950000-5980400	Strong transcription	Dnd41	blood
43	chr10:5950200-5975800	Strong transcription	Brain Germinal Matrix	brain
44	chr10:5950200-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:5950600-5964000	Strong transcription	Spleen	Spleen
46	chr10:5950600-5968600	Strong transcription	Osteobl	bone
47	chr10:5950600-5968800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr10:5950600-5973200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr10:5950600-5973600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr10:5950600-5974600	Strong transcription	Rectal Mucosa Donor 31	rectum

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