Variant report

Variant	rs1665982
Chromosome Location	chr3:47905079-47905080
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	chr3:47881404..47884302-chr3:47904180..47905829,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1013431	0.84[CEU][hapmap]
rs1060407	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1061003	0.86[EUR][1000 genomes]
rs11130148	0.81[TSI][hapmap]
rs11130152	0.87[CEU][hapmap]
rs1137524	0.82[EUR][1000 genomes]
rs11707679	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11712464	0.81[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12495204	0.81[TSI][hapmap]
rs12635438	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs13072132	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs13074973	0.84[CEU][hapmap]
rs13091913	0.84[TSI][hapmap]
rs13093830	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13094264	0.81[TSI][hapmap]
rs1486915	0.81[TSI][hapmap]
rs1486916	1.00[YRI][hapmap]
rs1684942	0.89[EUR][1000 genomes]
rs17079785	0.81[TSI][hapmap]
rs17290490	0.81[TSI][hapmap]
rs184388	0.82[EUR][1000 genomes]
rs2121754	0.84[CEU][hapmap]
rs2166770	0.84[CEU][hapmap]
rs2631721	0.85[EUR][1000 genomes]
rs319680	1.00[EUR][1000 genomes]
rs319681	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs319682	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs319683	0.83[YRI][hapmap]
rs319684	0.82[EUR][1000 genomes]
rs319685	0.82[EUR][1000 genomes]
rs319686	0.82[EUR][1000 genomes]
rs319689	0.83[EUR][1000 genomes]
rs319690	0.83[EUR][1000 genomes]
rs319692	0.85[EUR][1000 genomes]
rs319693	0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs319696	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs34025851	0.82[EUR][1000 genomes]
rs34448818	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs34507589	0.82[EUR][1000 genomes]
rs34675858	1.00[YRI][hapmap]
rs34750113	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35199727	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35314534	0.86[AFR][1000 genomes]
rs35943823	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732529	0.82[EUR][1000 genomes]
rs3772399	0.81[TSI][hapmap]
rs3888	0.81[TSI][hapmap]
rs3915654	0.81[TSI][hapmap]
rs4296617	0.84[AFR][1000 genomes]
rs4599334	0.84[CEU][hapmap]
rs4858810	0.80[CEU][hapmap]
rs4858851	0.81[TSI][hapmap]
rs4858860	0.81[TSI][hapmap]
rs4858863	0.87[ASW][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4858871	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs60446735	0.82[EUR][1000 genomes]
rs62260764	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6442082	0.81[TSI][hapmap]
rs6442091	0.84[AFR][1000 genomes]
rs6763824	1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs6768699	0.81[TSI][hapmap]
rs6772396	0.82[EUR][1000 genomes]
rs6776963	0.81[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6785669	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs6786001	0.81[TSI][hapmap]
rs7374516	0.84[CEU][hapmap]
rs7426976	0.81[CEU][hapmap]
rs7429990	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7430879	0.84[CEU][hapmap]
rs7430913	0.95[CEU][hapmap]
rs7618758	0.81[TSI][hapmap]
rs7619882	0.81[EUR][1000 genomes]
rs7629850	0.87[ASW][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7638103	0.81[TSI][hapmap]
rs7642590	0.87[ASW][hapmap];0.84[CEU][hapmap]
rs7645846	0.81[CEU][hapmap]
rs777014	0.82[EUR][1000 genomes]
rs777015	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs777017	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs796566	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs800762	0.89[EUR][1000 genomes]
rs810334	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs9681917	0.84[TSI][hapmap]
rs9812875	0.81[EUR][1000 genomes]
rs9850154	0.89[AFR][1000 genomes]
rs9862913	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
2	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1665982	ZNF589	cis	Nerve Tibial	GTEx
rs1665982	MRPS18AP1	cis	Thyroid	GTEx
rs1665982	ZNF589	cis	parietal	SCAN
rs1665982	CDC25A	cis	cerebellum	SCAN
rs1665982	ZNF589	cis	Esophagus Muscularis	GTEx
rs1665982	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs1665982	NME6	cis	Esophagus Muscularis	GTEx
rs1665982	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs1665982	ZNF589	cis	multi-tissue	Pritchard
rs1665982	ZNF589	cis	Artery Tibial	GTEx
rs1665982	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs1665982	HYAL2	cis	cerebellum	SCAN
rs1665982	MRPS18AP1	cis	Artery Tibial	GTEx
rs1665982	MRPS18AP1	cis	Nerve Tibial	GTEx
rs1665982	SMARCC1	cis	cerebellum	SCAN
rs1665982	ZNF589	cis	cerebellum	SCAN
rs1665982	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1665982	ZNF445	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
5	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
6	chr3:47869000-47918600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:47878800-47908400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:47884600-47918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:47885000-47914800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:47889800-47910000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:47889800-47912600	Weak transcription	Fetal Heart	heart
13	chr3:47891000-47908400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:47891200-47908600	Weak transcription	Fetal Kidney	kidney
15	chr3:47891400-47909600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:47891400-47912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:47892200-47906800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:47893600-47906600	Weak transcription	Small Intestine	intestine
19	chr3:47894200-47912200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:47894800-47907000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:47894800-47917400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:47894800-47919400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:47895800-47906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:47896600-47919600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:47896800-47913200	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:47899000-47906400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:47899000-47906800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:47899000-47906800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:47899000-47908400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:47899000-47908400	Weak transcription	Stomach Mucosa	stomach
31	chr3:47899000-47908600	Weak transcription	Hela-S3	cervix
32	chr3:47899000-47910800	Weak transcription	Fetal Brain Male	brain
33	chr3:47899000-47911200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:47899000-47919000	Weak transcription	Right Atrium	heart
35	chr3:47899200-47905200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:47899200-47905200	Weak transcription	K562	blood
37	chr3:47899200-47906400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:47899200-47906600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:47899200-47906600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:47899200-47906600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:47899400-47906800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:47899400-47906800	Weak transcription	Psoas Muscle	Psoas
43	chr3:47901200-47905400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:47901800-47906400	Weak transcription	HUVEC	blood vessel
45	chr3:47902200-47906200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:47902200-47906400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:47902200-47906400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:47902200-47906400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:47902200-47906800	Weak transcription	Colonic Mucosa	Colon
50	chr3:47902200-47908400	Weak transcription	Fetal Lung	lung

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