Variant report

Variant	rs11710199
Chromosome Location	chr3:47878078-47878079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47877782..47879462-chr3:47906492..47908037,2	K562	blood:
2	chr3:47865345..47867578-chr3:47877980..47880462,2	MCF-7	breast:
3	chr3:47868441..47869997-chr3:47876493..47878380,2	K562	blood:
4	chr3:47872432..47874998-chr3:47877284..47880049,4	K562	blood:
5	chr3:47871108..47875546-chr3:47876904..47881221,5	K562	blood:

Variant related genes	Relation type
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1013431	0.80[ASN][1000 genomes]
rs1061003	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130147	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11130148	0.81[EUR][1000 genomes]
rs11130150	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130152	0.86[AFR][1000 genomes]
rs11130154	0.86[AFR][1000 genomes]
rs1137524	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11708849	0.84[EUR][1000 genomes]
rs11712464	0.81[EUR][1000 genomes]
rs11714942	0.83[AFR][1000 genomes]
rs11927129	0.81[EUR][1000 genomes]
rs12495204	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13064183	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13074973	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13075457	0.87[AFR][1000 genomes]
rs13075795	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13077230	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079407	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13086149	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13091913	0.82[EUR][1000 genomes]
rs13094264	0.81[EUR][1000 genomes]
rs13098128	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1486915	0.86[EUR][1000 genomes]
rs1550914	0.82[ASN][1000 genomes]
rs1684942	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17079785	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17290490	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs184388	0.87[ASN][1000 genomes]
rs2047559	0.82[AFR][1000 genomes]
rs2053767	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2101398	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2121754	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2166770	0.82[ASN][1000 genomes]
rs2166772	0.80[ASN][1000 genomes]
rs2631721	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28637561	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2882668	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs319680	0.93[AFR][1000 genomes]
rs319682	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs319684	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs319685	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs319686	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs319687	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs319688	0.82[AFR][1000 genomes]
rs319689	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs319690	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs319691	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs319692	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs319693	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319694	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319695	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs319696	0.89[ASN][1000 genomes]
rs34025851	0.89[ASN][1000 genomes]
rs34249203	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34351471	0.85[AFR][1000 genomes]
rs34569417	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34906469	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35148469	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35582375	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35698005	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732529	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3772399	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3915654	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4293721	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4858851	0.80[EUR][1000 genomes]
rs4858853	0.83[EUR][1000 genomes]
rs4858857	0.85[EUR][1000 genomes]
rs4858860	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858863	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4858871	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5012971	0.83[AFR][1000 genomes]
rs55823596	0.84[EUR][1000 genomes]
rs56376646	0.81[EUR][1000 genomes]
rs60446735	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61181421	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62263561	0.84[EUR][1000 genomes]
rs62263575	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442079	0.81[EUR][1000 genomes]
rs6442081	0.81[EUR][1000 genomes]
rs6442082	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6442083	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6442085	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6442086	0.85[EUR][1000 genomes]
rs6442090	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6768699	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6770467	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6770477	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6772396	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6773208	0.82[ASN][1000 genomes]
rs6776963	0.86[EUR][1000 genomes]
rs6777632	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6783629	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6785669	0.80[EUR][1000 genomes]
rs6786001	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6792350	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792737	0.80[AFR][1000 genomes]
rs6806820	0.82[ASN][1000 genomes]
rs6806860	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72906488	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73085151	0.84[EUR][1000 genomes]
rs7374516	0.82[ASN][1000 genomes]
rs7426976	0.80[ASN][1000 genomes]
rs7427418	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7430879	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7430913	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7612219	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7618758	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7619882	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7627645	0.83[AFR][1000 genomes]
rs7629850	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7637372	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7637950	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7638103	0.81[EUR][1000 genomes]
rs7645846	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7649393	0.81[EUR][1000 genomes]
rs7649981	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7653368	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs777014	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs777015	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs796566	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs800762	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs810334	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9757517	0.82[EUR][1000 genomes]
rs9811277	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9812875	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9814961	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9842649	0.85[ASN][1000 genomes]
rs9846062	0.82[ASN][1000 genomes]
rs9850154	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9854454	0.82[ASN][1000 genomes]
rs9862913	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11710199	ZNF589	cis	Nerve Tibial	GTEx
rs11710199	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs11710199	MRPS18AP1	cis	Nerve Tibial	GTEx
rs11710199	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs11710199	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47882000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:47867800-47882000	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:47867800-47882400	Weak transcription	Small Intestine	intestine
4	chr3:47867800-47882400	Weak transcription	Stomach Mucosa	stomach
5	chr3:47867800-47882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:47867800-47899200	Strong transcription	Fetal Brain Female	brain
7	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:47868000-47882200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:47868000-47882800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:47868000-47903000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:47868200-47878600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:47868200-47879400	Weak transcription	Right Atrium	heart
14	chr3:47868200-47882000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:47868200-47882800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:47868200-47892200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:47868200-47902400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:47868400-47881800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:47868400-47882000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:47868400-47882000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:47868400-47884400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:47868400-47891000	Strong transcription	Fetal Muscle Leg	muscle
23	chr3:47868400-47891200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:47868400-47891400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:47868400-47899200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:47868400-47901200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:47868400-47902400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:47868400-47903000	Strong transcription	Placenta	Placenta
29	chr3:47868400-47903400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:47868400-47903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
33	chr3:47868600-47879400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:47868600-47880800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:47868600-47882400	Weak transcription	Fetal Heart	heart
36	chr3:47868600-47893600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:47868600-47899000	Strong transcription	Thymus	Thymus
38	chr3:47868600-47899200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:47868600-47899200	Strong transcription	Primary T cells from cord blood	blood
40	chr3:47868600-47899400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:47868600-47901800	Strong transcription	Fetal Intestine Large	intestine
42	chr3:47868600-47902200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:47868600-47902600	Strong transcription	Liver	Liver
44	chr3:47868600-47902800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
46	chr3:47868800-47880600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr3:47868800-47880600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:47868800-47880800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:47868800-47890400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:47868800-47894000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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