Variant report

Variant	rs1684942
Chromosome Location	chr3:47900703-47900704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47900580-47900887	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47895316..47897321-chr3:47900052..47901819,3	K562	blood:
2	chr3:47893361..47897321-chr3:47899658..47903190,4	K562	blood:
3	chr3:47899451..47902057-chr3:48195294..48197379,2	K562	blood:

Variant related genes	Relation type
MAP4	TF binding region

Extended variants
information (count: 150 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1013431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1060407	0.83[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061003	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130146	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11130148	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11130150	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11130152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11130154	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1137524	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707679	0.83[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710199	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11712464	0.93[JPT][hapmap]
rs12495204	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12635438	0.93[JPT][hapmap]
rs13063042	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs13064183	0.81[AFR][1000 genomes]
rs13074973	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075457	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13075795	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13077230	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13079407	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs13081701	0.80[EUR][1000 genomes]
rs13086149	0.83[AFR][1000 genomes]
rs13091913	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13093830	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094264	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13098128	0.82[AFR][1000 genomes]
rs1486915	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1530646	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1550914	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1665982	0.89[EUR][1000 genomes]
rs17079785	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17290490	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs184388	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2047559	1.00[YRI][hapmap]
rs2053767	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2101398	0.85[AFR][1000 genomes]
rs2121754	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2133601	0.94[CHB][hapmap];0.96[YRI][hapmap]
rs2140335	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2166770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2166772	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2351248	1.00[JPT][hapmap]
rs2631721	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637561	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882668	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs319680	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs319681	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319684	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319685	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319686	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319687	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs319688	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs319689	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs319690	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs319691	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs319692	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319693	0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319694	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs319695	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs319696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34025851	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34249203	0.82[ASN][1000 genomes]
rs34351471	0.82[AFR][1000 genomes]
rs34569417	0.86[AFR][1000 genomes]
rs34750113	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34906469	0.82[AFR][1000 genomes]
rs35148469	0.81[AFR][1000 genomes]
rs35199727	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35314534	0.82[EUR][1000 genomes]
rs35582375	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35698005	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35943823	0.88[EUR][1000 genomes]
rs3732529	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772399	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3888	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3915654	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4293721	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4296617	0.82[EUR][1000 genomes]
rs4392441	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4599334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858851	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4858860	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4858863	0.93[JPT][hapmap]
rs4858871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858876	0.82[ASN][1000 genomes]
rs4858887	0.81[EUR][1000 genomes]
rs5012971	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60446735	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61181421	0.89[AFR][1000 genomes]
rs62263575	0.84[ASN][1000 genomes]
rs6442082	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6442083	0.83[AFR][1000 genomes]
rs6442090	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442091	0.82[EUR][1000 genomes]
rs6768699	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6770467	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6770477	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6772301	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6772396	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773208	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776963	0.93[JPT][hapmap]
rs6777632	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6783629	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785669	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6786001	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6792350	0.81[ASN][1000 genomes]
rs6792497	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6806820	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806860	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs72906488	0.86[AFR][1000 genomes]
rs7374516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7426976	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7427418	0.94[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7429162	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7429990	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7430879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7430913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612219	0.81[AFR][1000 genomes]
rs7618758	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs7619882	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627645	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7629850	0.93[JPT][hapmap]
rs7637372	0.83[AFR][1000 genomes]
rs7637950	0.80[AFR][1000 genomes]
rs7638103	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7642590	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs7645846	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7649981	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7653368	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs777014	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs777015	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs777017	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs796566	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs800762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs810334	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9681917	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9811277	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812875	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814961	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9842649	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9846062	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9854454	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9860485	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9862913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1684942	ZNF589	cis	Nerve Tibial	GTEx
rs1684942	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs1684942	MRPS18AP1	cis	Nerve Tibial	GTEx
rs1684942	ZNF589	cis	Whole Blood	GTEx
rs1684942	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1684942	MRPS18AP1	cis	Muscle Skeletal	GTEx

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	chr3:47868000-47903000	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47868200-47902400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:47868400-47901200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:47868400-47902400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:47868400-47903000	Strong transcription	Placenta	Placenta
8	chr3:47868400-47903400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:47868400-47903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
12	chr3:47868600-47901800	Strong transcription	Fetal Intestine Large	intestine
13	chr3:47868600-47902200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:47868600-47902600	Strong transcription	Liver	Liver
15	chr3:47868600-47902800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
17	chr3:47868800-47902000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:47868800-47902200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:47868800-47902400	Strong transcription	Osteobl	bone
20	chr3:47869000-47902400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:47869000-47918600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:47869200-47902200	Strong transcription	Dnd41	blood
23	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:47871800-47901600	Strong transcription	Brain Germinal Matrix	brain
25	chr3:47877200-47903400	Strong transcription	Lung	lung
26	chr3:47877400-47902600	Strong transcription	Spleen	Spleen
27	chr3:47878800-47908400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:47879800-47902400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:47881200-47902200	Strong transcription	Colon Smooth Muscle	Colon
30	chr3:47881600-47902200	Strong transcription	Esophagus	oesophagus
31	chr3:47881600-47902200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr3:47881600-47903400	Strong transcription	NHEK	skin
33	chr3:47881800-47902200	Strong transcription	Right Ventricle	heart
34	chr3:47882000-47902200	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr3:47882000-47902200	Strong transcription	NHLF	lung
36	chr3:47882200-47903000	Strong transcription	Ovary	ovary
37	chr3:47882200-47903600	Strong transcription	Left Ventricle	heart
38	chr3:47884600-47918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:47885000-47902200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:47885000-47914800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:47889800-47910000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:47889800-47912600	Weak transcription	Fetal Heart	heart
43	chr3:47891000-47908400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:47891200-47903200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:47891200-47908600	Weak transcription	Fetal Kidney	kidney
46	chr3:47891400-47909600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:47891400-47912000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:47891600-47903600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:47892000-47902600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr3:47892200-47906800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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