Variant report

Variant	rs730884
Chromosome Location	chr2:55846871-55846872
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55846832-55847132	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55846036..55847829-chr2:55873560..55876152,3	K562	blood:
2	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
3	chr2:55845275..55847536-chr2:55874365..55876152,2	K562	blood:
4	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC104-3	chr2:55845115-55846902	NONHSAT070800

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000138035	Chromatin interaction
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10195281	0.84[AFR][1000 genomes]
rs10200159	0.83[AFR][1000 genomes]
rs10203953	0.82[AFR][1000 genomes]
rs1037508	0.90[ASN][1000 genomes]
rs10427222	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1045910	0.84[ASN][1000 genomes]
rs11890141	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11900763	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12463766	0.90[ASN][1000 genomes]
rs12619756	0.83[ASN][1000 genomes]
rs12989898	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13016772	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028892	0.91[ASN][1000 genomes]
rs13403782	0.85[ASN][1000 genomes]
rs1563201	0.82[ASN][1000 genomes]
rs2168097	0.82[ASN][1000 genomes]
rs2586946	0.89[ASN][1000 genomes]
rs2586948	0.87[ASN][1000 genomes]
rs2586965	0.88[ASN][1000 genomes]
rs2627758	0.88[ASN][1000 genomes]
rs2627763	0.88[ASN][1000 genomes]
rs2627778	0.83[ASN][1000 genomes]
rs2627783	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748945	0.95[ASN][1000 genomes]
rs3748955	0.88[AFR][1000 genomes]
rs3816489	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233962	0.90[ASN][1000 genomes]
rs4671248	0.92[ASN][1000 genomes]
rs4671250	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62165178	0.91[ASN][1000 genomes]
rs6545505	0.83[ASN][1000 genomes]
rs6545510	0.84[AFR][1000 genomes]
rs6712314	0.84[AFR][1000 genomes]
rs6731927	0.82[ASN][1000 genomes]
rs6736996	0.84[AFR][1000 genomes]
rs6745430	0.90[AFR][1000 genomes]
rs6760959	0.83[AFR][1000 genomes]
rs736345	0.94[AFR][1000 genomes]
rs744514	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571482	0.87[ASN][1000 genomes]
rs7574398	0.83[AFR][1000 genomes]
rs7574409	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7585484	0.82[ASN][1000 genomes]
rs7605486	0.82[ASN][1000 genomes]
rs7605504	0.83[ASN][1000 genomes]
rs782589	0.88[ASN][1000 genomes]
rs782591	0.89[ASN][1000 genomes]
rs782593	0.89[ASN][1000 genomes]
rs782597	0.82[ASN][1000 genomes]
rs782598	0.89[ASN][1000 genomes]
rs782603	0.88[ASN][1000 genomes]
rs782612	0.88[ASN][1000 genomes]
rs782648	0.84[ASN][1000 genomes]
rs782651	0.84[ASN][1000 genomes]
rs9309267	0.87[AFR][1000 genomes]
rs9309268	0.83[AFR][1000 genomes]
rs9636439	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs730884	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs730884	SMEK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55842800-55847800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:55845000-55847400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55846000-55847600	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr2:55846200-55847000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr2:55846200-55847000	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr2:55846200-55847400	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr2:55846200-55847400	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr2:55846200-55847400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr2:55846200-55847600	Enhancers	Placenta	Placenta
10	chr2:55846200-55847800	Flanking Active TSS	Hela-S3	cervix
11	chr2:55846400-55847000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:55846400-55847400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr2:55846400-55848000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:55846400-55848000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
16	chr2:55846600-55847000	Enhancers	Stomach Mucosa	stomach
17	chr2:55846600-55847200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr2:55846600-55847200	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:55846600-55847400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr2:55846600-55847400	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:55846600-55847400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:55846600-55847400	Enhancers	Lung	lung
23	chr2:55846600-55847600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:55846600-55847600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:55846600-55847600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:55846600-55847600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:55846600-55847600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:55846600-55847600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr2:55846600-55847600	Enhancers	Fetal Brain Male	brain
30	chr2:55846600-55847600	Enhancers	Fetal Lung	lung
31	chr2:55846600-55847600	Enhancers	Fetal Muscle Leg	muscle
32	chr2:55846600-55847600	Enhancers	Gastric	stomach
33	chr2:55846600-55847600	Enhancers	Left Ventricle	heart
34	chr2:55846600-55847600	Enhancers	Right Atrium	heart
35	chr2:55846600-55847600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:55846600-55847600	Enhancers	Spleen	Spleen
37	chr2:55846600-55847800	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:55846600-55847800	Enhancers	Brain Substantia Nigra	brain
39	chr2:55846600-55847800	Genic enhancers	Fetal Stomach	stomach
40	chr2:55846600-55847800	Enhancers	Right Ventricle	heart
41	chr2:55846600-55847800	Enhancers	HUVEC	blood vessel
42	chr2:55846600-55847800	Enhancers	NH-A	brain
43	chr2:55846600-55847800	Enhancers	NHEK	skin
44	chr2:55846600-55848000	Enhancers	Small Intestine	intestine
45	chr2:55846600-55848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:55846600-55848600	Weak transcription	Esophagus	oesophagus
47	chr2:55846600-55848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:55846600-55849000	Enhancers	Colon Smooth Muscle	Colon
49	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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