Variant report

Variant	rs319681
Chromosome Location	chr3:47920240-47920241
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	chr3:47919145..47920888-chr3:47933987..47935579,2	K562	blood:
2	chr3:47915163..47917361-chr3:47919966..47922770,2	K562	blood:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1013431	0.84[EUR][1000 genomes]
rs1060407	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061003	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130150	0.82[ASN][1000 genomes]
rs11130152	0.81[EUR][1000 genomes]
rs11130154	0.84[EUR][1000 genomes]
rs1137524	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11707679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13074973	0.84[EUR][1000 genomes]
rs13075457	0.82[EUR][1000 genomes]
rs13075795	0.83[EUR][1000 genomes]
rs13077230	0.82[ASN][1000 genomes]
rs13081701	0.82[EUR][1000 genomes]
rs13093830	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530646	0.84[EUR][1000 genomes]
rs1550914	0.84[EUR][1000 genomes]
rs1665982	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1684942	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17290490	0.82[ASN][1000 genomes]
rs184388	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2053767	0.84[EUR][1000 genomes]
rs2121754	0.84[EUR][1000 genomes]
rs2166770	0.84[EUR][1000 genomes]
rs2166772	0.84[EUR][1000 genomes]
rs2631721	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28637561	0.84[EUR][1000 genomes]
rs2882668	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319680	0.84[EUR][1000 genomes]
rs319682	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319684	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319685	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319686	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319687	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs319688	0.92[EUR][1000 genomes]
rs319689	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319690	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs319691	0.92[EUR][1000 genomes]
rs319692	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319693	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs319694	0.82[ASN][1000 genomes]
rs319695	0.93[ASN][1000 genomes]
rs319696	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34025851	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34750113	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35199727	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35314534	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35582375	0.82[ASN][1000 genomes]
rs35689209	0.80[EUR][1000 genomes]
rs35943823	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3732529	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4293721	0.84[EUR][1000 genomes]
rs4296617	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4392441	0.83[EUR][1000 genomes]
rs4599334	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858863	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4858871	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858876	0.80[EUR][1000 genomes]
rs4858887	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5012971	0.83[EUR][1000 genomes]
rs60446735	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442090	0.84[EUR][1000 genomes]
rs6442091	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442094	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442096	0.82[AMR][1000 genomes]
rs6770467	0.84[EUR][1000 genomes]
rs6770477	0.84[EUR][1000 genomes]
rs6772396	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773208	0.83[EUR][1000 genomes]
rs6783629	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6791834	0.81[EUR][1000 genomes]
rs6803741	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6806820	0.83[EUR][1000 genomes]
rs7374516	0.84[EUR][1000 genomes]
rs7426976	0.84[EUR][1000 genomes]
rs7427418	0.84[EUR][1000 genomes]
rs7429990	0.84[EUR][1000 genomes]
rs7430879	0.84[EUR][1000 genomes]
rs7430913	0.84[EUR][1000 genomes]
rs7431567	0.81[AMR][1000 genomes]
rs7619882	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7620736	0.81[EUR][1000 genomes]
rs7627645	0.83[EUR][1000 genomes]
rs7629850	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7642590	0.82[EUR][1000 genomes]
rs7649981	0.84[EUR][1000 genomes]
rs7653368	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs777014	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs777015	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs777017	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs796566	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs800762	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs810334	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9811277	0.84[EUR][1000 genomes]
rs9812875	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9814961	0.84[EUR][1000 genomes]
rs9842649	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9846062	0.84[EUR][1000 genomes]
rs9850154	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9854454	0.84[EUR][1000 genomes]
rs9860485	0.82[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	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs319681	NME6	cis	Esophagus Muscularis	GTEx
rs319681	MRPS18AP1	cis	Nerve Tibial	GTEx
rs319681	ZNF589	cis	Whole Blood	GTEx
rs319681	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs319681	MRPS18AP1	cis	Artery Tibial	GTEx
rs319681	MRPS18AP1	cis	Thyroid	GTEx
rs319681	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs319681	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs319681	ZNF589	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 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	chr3:47910600-47926400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:47912000-47926200	Weak transcription	Fetal Brain Male	brain
7	chr3:47912600-47939200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:47913600-47932200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:47913600-47932200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:47913600-47932600	Weak transcription	Stomach Mucosa	stomach
11	chr3:47914200-47930400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:47915000-47925800	Weak transcription	Fetal Brain Female	brain
13	chr3:47915000-47932000	Weak transcription	Ovary	ovary
14	chr3:47915000-47932600	Weak transcription	Aorta	Aorta
15	chr3:47915000-47939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:47916800-47930200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:47916800-47931800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:47917000-47926400	Weak transcription	Fetal Kidney	kidney
19	chr3:47917200-47926000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:47917200-47926000	Weak transcription	NHLF	lung
21	chr3:47917200-47926200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:47917200-47930400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:47917200-47930800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:47917200-47931800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:47917200-47932200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:47917200-47932200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:47917400-47922200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:47917400-47922200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:47917400-47922800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:47917400-47924000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:47917400-47924000	Weak transcription	HSMMtube	muscle
32	chr3:47917400-47926000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:47917400-47926000	Weak transcription	Brain Germinal Matrix	brain
34	chr3:47917400-47926000	Weak transcription	Colonic Mucosa	Colon
35	chr3:47917400-47926000	Weak transcription	Esophagus	oesophagus
36	chr3:47917400-47926000	Weak transcription	Fetal Thymus	thymus
37	chr3:47917400-47926000	Weak transcription	Lung	lung
38	chr3:47917400-47926000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:47917400-47928800	Weak transcription	Pancreas	Pancrea
40	chr3:47917400-47930000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:47917400-47931600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:47917400-47931800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:47917400-47932200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:47917400-47932200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:47917400-47932200	Weak transcription	NHDF-Ad	bronchial
46	chr3:47917400-47932800	Weak transcription	Gastric	stomach
47	chr3:47917600-47922000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:47917600-47930800	Weak transcription	Hela-S3	cervix
49	chr3:47917600-47932600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:47917600-47957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links