Variant report

Variant	rs319680
Chromosome Location	chr3:47898307-47898308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1013431	0.84[CEU][hapmap]
rs1060407	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1061003	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11130146	0.89[LWK][hapmap];0.96[YRI][hapmap]
rs11130148	0.81[TSI][hapmap]
rs11130150	0.92[AFR][1000 genomes]
rs11130152	0.87[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs11130154	0.90[AFR][1000 genomes]
rs1137524	0.82[EUR][1000 genomes]
rs11707679	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11710199	0.93[AFR][1000 genomes]
rs11712464	0.81[TSI][hapmap]
rs12495204	0.83[ASW][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs13061412	0.82[CEU][hapmap]
rs13063042	0.87[LWK][hapmap];0.92[YRI][hapmap]
rs13064183	0.81[AFR][1000 genomes]
rs13072132	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap]
rs13074973	0.84[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs13075457	0.90[AFR][1000 genomes]
rs13075795	0.90[AFR][1000 genomes]
rs13077230	0.93[AFR][1000 genomes]
rs13079407	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs13086149	0.82[AFR][1000 genomes]
rs13091913	0.84[TSI][hapmap]
rs13093830	0.82[EUR][1000 genomes]
rs13094264	0.81[TSI][hapmap]
rs13098128	0.81[AFR][1000 genomes]
rs1486915	0.81[TSI][hapmap]
rs1665982	1.00[EUR][1000 genomes]
rs1684942	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17079785	0.95[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs17290490	0.83[ASW][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs184388	0.82[EUR][1000 genomes]
rs2047559	0.96[YRI][hapmap]
rs2053767	0.90[AFR][1000 genomes]
rs2101398	0.84[AFR][1000 genomes]
rs2121754	0.84[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2133601	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs2140335	0.96[YRI][hapmap]
rs2166770	0.84[CEU][hapmap]
rs2631721	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs28637561	0.90[AFR][1000 genomes]
rs2882668	0.93[AFR][1000 genomes]
rs319681	0.84[EUR][1000 genomes]
rs319682	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs319684	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs319685	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs319686	0.82[EUR][1000 genomes]
rs319687	0.97[AFR][1000 genomes]
rs319688	0.84[AFR][1000 genomes]
rs319689	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs319690	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs319691	0.94[AFR][1000 genomes]
rs319692	0.85[EUR][1000 genomes]
rs319693	0.81[TSI][hapmap]
rs319694	0.83[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs319696	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs34025851	0.82[EUR][1000 genomes]
rs34351471	0.81[AFR][1000 genomes]
rs34448818	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap]
rs34507589	0.82[EUR][1000 genomes]
rs34569417	0.85[AFR][1000 genomes]
rs34750113	0.81[EUR][1000 genomes]
rs34906469	0.81[AFR][1000 genomes]
rs35148469	0.81[AFR][1000 genomes]
rs35199727	0.82[EUR][1000 genomes]
rs35582375	0.93[AFR][1000 genomes]
rs35698005	0.88[AFR][1000 genomes]
rs35943823	0.99[EUR][1000 genomes]
rs3732529	0.82[EUR][1000 genomes]
rs3772399	0.83[ASW][hapmap];0.87[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs3888	0.81[TSI][hapmap]
rs3915654	0.83[ASW][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs4293721	0.90[AFR][1000 genomes]
rs4599334	0.84[CEU][hapmap]
rs4858810	0.80[CEU][hapmap]
rs4858851	0.81[TSI][hapmap]
rs4858860	0.81[TSI][hapmap]
rs4858863	0.81[TSI][hapmap]
rs4858871	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs5012971	0.87[AFR][1000 genomes]
rs60446735	0.82[EUR][1000 genomes]
rs61181421	0.88[AFR][1000 genomes]
rs62260764	0.85[EUR][1000 genomes]
rs6442082	0.83[ASW][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6442083	0.82[AFR][1000 genomes]
rs6442090	0.90[AFR][1000 genomes]
rs6763824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs6768699	0.83[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs6770467	0.90[AFR][1000 genomes]
rs6770477	0.90[AFR][1000 genomes]
rs6772301	0.92[YRI][hapmap]
rs6772396	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6776963	0.81[TSI][hapmap]
rs6777632	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6785669	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs6786001	0.83[ASW][hapmap];0.89[LWK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs6792497	0.96[YRI][hapmap]
rs6806860	0.95[LWK][hapmap];0.96[YRI][hapmap]
rs72906488	0.85[AFR][1000 genomes]
rs7374516	0.84[CEU][hapmap];0.84[LWK][hapmap]
rs7426976	0.81[CEU][hapmap]
rs7427418	0.88[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs7429990	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7430879	0.88[ASW][hapmap];0.84[CEU][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7430913	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7612219	0.81[AFR][1000 genomes]
rs7618758	0.83[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap]
rs7619882	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7627645	0.86[AFR][1000 genomes]
rs7629850	0.81[TSI][hapmap]
rs7637372	0.82[AFR][1000 genomes]
rs7638103	0.81[TSI][hapmap]
rs7645846	0.81[CEU][hapmap];0.96[YRI][hapmap]
rs7649981	0.90[AFR][1000 genomes]
rs7653368	0.94[AFR][1000 genomes]
rs777014	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs777015	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs777017	0.82[EUR][1000 genomes]
rs796566	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs800762	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs810334	0.88[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9681917	0.84[TSI][hapmap]
rs9811277	0.90[AFR][1000 genomes]
rs9812875	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9814961	0.90[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
rs319680	HYAL2	cis	cerebellum	SCAN
rs319680	GNAI2	cis	parietal	SCAN
rs319680	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs319680	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs319680	ATRIP	cis	cerebellum	SCAN
rs319680	ZNF589	cis	Artery Tibial	GTEx
rs319680	SMARCC1	cis	cerebellum	SCAN
rs319680	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs319680	ZNF589	cis	Esophagus Muscularis	GTEx
rs319680	ZNF445	cis	cerebellum	SCAN
rs319680	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs319680	CDC25A	cis	cerebellum	SCAN
rs319680	ZNF589	cis	parietal	SCAN
rs319680	ALS2CL	cis	parietal	SCAN
rs319680	CDC25A	cis	Muscle Skeletal	GTEx
rs319680	ZNF589	cis	cerebellum	SCAN
rs319680	MRPS18AP1	cis	Nerve Tibial	GTEx
rs319680	ZNF589	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47899200	Strong transcription	Fetal Brain Female	brain
2	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:47868000-47903000	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47868200-47902400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:47868400-47899200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr3:47868400-47901200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:47868400-47902400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:47868400-47903000	Strong transcription	Placenta	Placenta
10	chr3:47868400-47903400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:47868400-47903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
14	chr3:47868600-47899000	Strong transcription	Thymus	Thymus
15	chr3:47868600-47899200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr3:47868600-47899200	Strong transcription	Primary T cells from cord blood	blood
17	chr3:47868600-47899400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:47868600-47901800	Strong transcription	Fetal Intestine Large	intestine
19	chr3:47868600-47902200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:47868600-47902600	Strong transcription	Liver	Liver
21	chr3:47868600-47902800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
23	chr3:47868800-47902000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:47868800-47902200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:47868800-47902400	Strong transcription	Osteobl	bone
26	chr3:47869000-47899400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:47869000-47902400	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:47869000-47918600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:47869200-47902200	Strong transcription	Dnd41	blood
30	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:47871200-47899200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:47871400-47899200	Strong transcription	Fetal Thymus	thymus
33	chr3:47871600-47899200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:47871800-47899200	Strong transcription	Gastric	stomach
35	chr3:47871800-47901600	Strong transcription	Brain Germinal Matrix	brain
36	chr3:47872000-47899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:47872200-47899200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr3:47876000-47899000	Strong transcription	Rectal Smooth Muscle	rectum
39	chr3:47877200-47903400	Strong transcription	Lung	lung
40	chr3:47877400-47902600	Strong transcription	Spleen	Spleen
41	chr3:47878400-47899000	Strong transcription	Colonic Mucosa	Colon
42	chr3:47878800-47908400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:47879800-47902400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:47880400-47898600	Strong transcription	Brain Hippocampus Middle	brain
45	chr3:47881200-47902200	Strong transcription	Colon Smooth Muscle	Colon
46	chr3:47881600-47899200	Strong transcription	Pancreas	Pancrea
47	chr3:47881600-47902200	Strong transcription	Esophagus	oesophagus
48	chr3:47881600-47902200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:47881600-47903400	Strong transcription	NHEK	skin
50	chr3:47881800-47902200	Strong transcription	Right Ventricle	heart

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