Variant report

Variant	rs319688
Chromosome Location	chr3:47928786-47928787
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	chr3:47928304..47929977-chr3:47930679..47933276,2	K562	blood:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1013431	0.83[EUR][1000 genomes]
rs1060407	0.94[EUR][1000 genomes]
rs1061003	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130150	0.81[AFR][1000 genomes]
rs11130152	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11130154	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1137524	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11707679	0.94[EUR][1000 genomes]
rs11710199	0.82[AFR][1000 genomes]
rs13074973	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13075457	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13075795	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13077230	0.82[AFR][1000 genomes]
rs13081701	0.83[EUR][1000 genomes]
rs13093830	0.94[EUR][1000 genomes]
rs1530646	0.84[EUR][1000 genomes]
rs1550914	0.84[EUR][1000 genomes]
rs1684942	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17290490	0.85[AFR][1000 genomes]
rs184388	0.94[EUR][1000 genomes]
rs2053767	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2121754	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2166770	0.84[EUR][1000 genomes]
rs2166772	0.84[EUR][1000 genomes]
rs2631721	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28637561	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2882668	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs319680	0.84[AFR][1000 genomes]
rs319681	0.92[EUR][1000 genomes]
rs319682	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs319684	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs319685	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs319686	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs319687	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs319689	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs319690	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs319691	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs319692	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs319694	0.85[AFR][1000 genomes]
rs319696	0.94[EUR][1000 genomes]
rs34025851	0.94[EUR][1000 genomes]
rs34750113	0.91[EUR][1000 genomes]
rs35199727	0.94[EUR][1000 genomes]
rs35314534	0.84[EUR][1000 genomes]
rs35582375	0.82[AFR][1000 genomes]
rs3732529	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4293721	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4296617	0.84[EUR][1000 genomes]
rs4392441	0.83[EUR][1000 genomes]
rs4599334	0.84[EUR][1000 genomes]
rs4858871	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4858887	0.83[EUR][1000 genomes]
rs5012971	0.83[EUR][1000 genomes]
rs60446735	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6442090	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6442091	0.84[EUR][1000 genomes]
rs6770467	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6770477	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6772396	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6773208	0.82[EUR][1000 genomes]
rs6783629	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6791834	0.80[EUR][1000 genomes]
rs6806820	0.83[EUR][1000 genomes]
rs7374516	0.84[EUR][1000 genomes]
rs7426976	0.84[EUR][1000 genomes]
rs7427418	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7430879	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7430913	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7619882	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7620736	0.80[EUR][1000 genomes]
rs7627645	0.83[EUR][1000 genomes]
rs7642590	0.81[EUR][1000 genomes]
rs7649981	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7653368	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs777014	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs777015	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs777017	0.94[EUR][1000 genomes]
rs796566	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs800762	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs810334	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9811277	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9812875	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9814961	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9842649	0.91[EUR][1000 genomes]
rs9846062	0.83[EUR][1000 genomes]
rs9854454	0.84[EUR][1000 genomes]
rs9860485	0.81[EUR][1000 genomes]
rs9862913	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1796001	chr3:47912703-48012797	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1826403	chr3:47912703-48012797	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1000817	chr3:47927730-48032401	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs319688	MAP4	cis	brain	BrainEAC
rs319688	MRPS18AP1	cis	Nerve Tibial	GTEx
rs319688	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs319688	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs319688	ZNF589	cis	Nerve Tibial	GTEx
rs319688	MAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:47907200-47931600	Weak transcription	Psoas Muscle	Psoas
3	chr3:47910200-47957000	Weak transcription	Small Intestine	intestine
4	chr3:47910200-47978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:47912600-47939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:47913600-47932200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:47913600-47932200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:47913600-47932600	Weak transcription	Stomach Mucosa	stomach
9	chr3:47914200-47930400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:47915000-47932000	Weak transcription	Ovary	ovary
11	chr3:47915000-47932600	Weak transcription	Aorta	Aorta
12	chr3:47915000-47939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:47916800-47930200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:47916800-47931800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:47917200-47930400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:47917200-47930800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:47917200-47931800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:47917200-47932200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:47917200-47932200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:47917400-47928800	Weak transcription	Pancreas	Pancrea
21	chr3:47917400-47930000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:47917400-47931600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:47917400-47931800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:47917400-47932200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:47917400-47932200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:47917400-47932200	Weak transcription	NHDF-Ad	bronchial
27	chr3:47917400-47932800	Weak transcription	Gastric	stomach
28	chr3:47917600-47930800	Weak transcription	Hela-S3	cervix
29	chr3:47917600-47932600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:47917600-47957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:47918200-47932400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:47918600-47932200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:47918600-47932800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:47919200-47931600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:47919400-47930400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:47919600-47930200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:47919600-47930400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:47919600-47930600	Weak transcription	Right Atrium	heart
39	chr3:47919600-47931000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:47919600-47932200	Weak transcription	Placenta	Placenta
41	chr3:47919600-47932200	Weak transcription	Spleen	Spleen
42	chr3:47919600-47932400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr3:47919600-47932400	Weak transcription	Dnd41	blood
44	chr3:47919600-47932400	Weak transcription	NH-A	brain
45	chr3:47919600-47933200	Weak transcription	K562	blood
46	chr3:47919800-47930200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:47919800-47930200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:47919800-47937000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:47920200-47930200	Weak transcription	Brain Substantia Nigra	brain
50	chr3:47920200-47930400	Weak transcription	Brain Hippocampus Middle	brain

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