Variant report

Variant	rs2046402
Chromosome Location	chr4:85762385-85762386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10007879	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10029496	0.86[AMR][1000 genomes]
rs10856851	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10856852	0.84[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap]
rs11097024	0.81[EUR][1000 genomes]
rs11097026	0.81[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11730981	0.86[AMR][1000 genomes]
rs12498637	0.85[AMR][1000 genomes]
rs12501525	0.84[EUR][1000 genomes]
rs12503215	0.86[AMR][1000 genomes]
rs12506456	0.86[AMR][1000 genomes]
rs12510410	0.85[AMR][1000 genomes]
rs12511112	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12648852	0.83[AMR][1000 genomes]
rs13109918	0.85[AMR][1000 genomes]
rs13114115	0.91[AMR][1000 genomes]
rs13118671	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13141322	0.91[AMR][1000 genomes]
rs13145705	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1385263	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1484660	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1484661	0.91[JPT][hapmap]
rs1508670	0.81[JPT][hapmap]
rs17009247	0.81[EUR][1000 genomes]
rs17009249	0.81[EUR][1000 genomes]
rs17009317	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs17009334	0.90[JPT][hapmap]
rs17009341	0.94[ASW][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs2046404	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2170935	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2218323	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs2869216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098928	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs3747680	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs4131745	0.90[AMR][1000 genomes]
rs4376130	0.81[AMR][1000 genomes]
rs4464556	0.86[AMR][1000 genomes]
rs4529041	0.84[EUR][1000 genomes]
rs4533765	0.86[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap]
rs4624645	0.86[AMR][1000 genomes]
rs6531775	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531777	0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes]
rs6531782	0.83[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap]
rs67045782	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6825852	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6829807	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6833661	0.83[AMR][1000 genomes]
rs6835046	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6838727	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs6847067	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6847564	0.95[JPT][hapmap]
rs6847811	0.86[AMR][1000 genomes]
rs6857555	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6858666	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72664926	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72664934	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664952	0.84[AMR][1000 genomes]
rs7654035	0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs7661609	0.94[ASW][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs7663580	0.84[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap]
rs7685537	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7694949	0.94[ASW][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs7699226	0.82[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes]
rs9684737	0.85[AMR][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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv427684	chr4:85668487-85863446	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2046402	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85697400-85772800	Weak transcription	Small Intestine	intestine
2	chr4:85701600-85783000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:85705400-85770000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:85708600-85777400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:85709000-85769600	Weak transcription	Right Ventricle	heart
6	chr4:85709000-85781600	Weak transcription	Esophagus	oesophagus
7	chr4:85709200-85770200	Weak transcription	Psoas Muscle	Psoas
8	chr4:85722200-85787600	Weak transcription	Gastric	stomach
9	chr4:85722400-85762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:85723000-85821000	Weak transcription	Pancreas	Pancrea
11	chr4:85723200-85770400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:85723200-85777000	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:85724000-85781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:85724000-85786600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:85724200-85769600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:85727800-85783200	Weak transcription	Colonic Mucosa	Colon
17	chr4:85731400-85769600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:85731400-85791600	Weak transcription	Lung	lung
19	chr4:85731800-85769600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:85735800-85777000	Weak transcription	Aorta	Aorta
21	chr4:85736400-85769600	Weak transcription	A549	lung
22	chr4:85736400-85790600	Weak transcription	NHEK	skin
23	chr4:85739400-85777000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:85742600-85783200	Weak transcription	Fetal Brain Male	brain
25	chr4:85742800-85769600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr4:85742800-85777000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:85747200-85769600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:85747800-85768000	Weak transcription	HepG2	liver
29	chr4:85749400-85769600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:85750400-85769600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:85751600-85783000	Weak transcription	Stomach Mucosa	stomach
32	chr4:85751800-85770000	Weak transcription	HMEC	breast
33	chr4:85752000-85769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:85752000-85769600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:85752200-85768000	Weak transcription	NHDF-Ad	bronchial
36	chr4:85753200-85783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:85754400-85763200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:85755000-85769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:85755200-85762400	Strong transcription	HSMM	muscle
40	chr4:85755200-85764200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:85755600-85763400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:85755800-85762400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:85756000-85763000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:85756600-85762400	Strong transcription	Liver	Liver
45	chr4:85756600-85769600	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:85757200-85763000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:85757200-85767600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:85757600-85769600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:85759200-85762400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:85759400-85763000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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