Variant report

Variant	rs17086909
Chromosome Location	chr4:57364041-57364042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57363740..57365752-chr4:57366897..57368422,2	K562	blood:
2	chr4:57344872..57347241-chr4:57362443..57365516,3	K562	blood:
3	chr4:57356189..57358476-chr4:57362362..57364129,2	K562	blood:
4	chr4:57343541..57346949-chr4:57360480..57364224,4	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10212643	0.83[EUR][1000 genomes]
rs1140982	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1142851	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940993	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12640212	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12643989	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643996	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644498	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649799	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650288	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1579019	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086759	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086773	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086801	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086804	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086830	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086838	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086868	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086919	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271924	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34398021	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733326	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796539	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796540	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796549	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796550	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4076103	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55778537	0.82[ASN][1000 genomes]
rs55903333	0.82[ASN][1000 genomes]
rs55909588	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56129706	0.82[ASN][1000 genomes]
rs56296497	0.82[ASN][1000 genomes]
rs56362514	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57245446	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58654038	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59153415	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59686671	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59764923	0.80[ASN][1000 genomes]
rs59828502	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831869	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7437839	0.85[EUR][1000 genomes]
rs7658340	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7688482	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086909	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
2	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:57335800-57365600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:57336000-57364200	Strong transcription	Osteobl	bone
9	chr4:57336000-57369400	Strong transcription	Liver	Liver
10	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:57336200-57365000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
17	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
18	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:57336400-57364800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:57336400-57365400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:57336600-57364200	Strong transcription	Dnd41	blood
26	chr4:57336600-57365400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:57337200-57365400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:57337200-57369200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:57337600-57364800	Strong transcription	Fetal Intestine Large	intestine
31	chr4:57337800-57365600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr4:57337800-57369200	Strong transcription	Adipose Nuclei	Adipose
33	chr4:57337800-57369400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:57338000-57365000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:57338200-57364200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:57340600-57366600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:57340800-57369000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:57343200-57364200	Strong transcription	NH-A	brain
42	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
43	chr4:57347000-57365600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:57349000-57364800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:57349600-57364200	Strong transcription	HSMM	muscle
46	chr4:57350200-57365400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:57350600-57364200	Strong transcription	Brain Germinal Matrix	brain
48	chr4:57350600-57364200	Strong transcription	Fetal Brain Female	brain
49	chr4:57352000-57371400	Weak transcription	Gastric	stomach
50	chr4:57352000-57371400	Weak transcription	Spleen	Spleen

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