Variant report

Variant	rs4952260
Chromosome Location	chr2:32534899-32534900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YIPF4-1	chr2:32534100-32537281	XLOC_001417

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1046602	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470951	0.83[EUR][1000 genomes]
rs12475684	0.89[EUR][1000 genomes]
rs17011943	0.91[EUR][1000 genomes]
rs17011947	0.83[EUR][1000 genomes]
rs35368935	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952257	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952259	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55788900	0.89[EUR][1000 genomes]
rs57813560	0.89[EUR][1000 genomes]
rs61045200	1.00[ASN][1000 genomes]
rs61439415	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134039	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134043	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134044	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134045	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134050	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134052	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134054	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134059	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62136263	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62136264	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62136276	0.87[EUR][1000 genomes]
rs62136278	0.89[EUR][1000 genomes]
rs62136279	0.87[EUR][1000 genomes]
rs62136280	0.83[EUR][1000 genomes]
rs62136282	0.83[EUR][1000 genomes]
rs62136284	0.83[EUR][1000 genomes]
rs62136285	0.83[EUR][1000 genomes]
rs62136286	0.83[EUR][1000 genomes]
rs62136287	0.80[EUR][1000 genomes]
rs62136302	0.85[EUR][1000 genomes]
rs72798728	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798733	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798784	0.80[EUR][1000 genomes]
rs7609320	0.83[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	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers 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 target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv1002120	chr2:32470452-32539443	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1004279	chr2:32470452-32543369	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv533153	chr2:32514528-33249136	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv979327	chr2:32532575-32554303	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32504000-32537600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:32504000-32540200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:32504000-32549400	Weak transcription	HSMMtube	muscle
4	chr2:32504800-32537600	Weak transcription	Fetal Brain Male	brain
5	chr2:32507800-32550000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:32514000-32553000	Weak transcription	Small Intestine	intestine
7	chr2:32514200-32555800	Weak transcription	Colonic Mucosa	Colon
8	chr2:32514800-32541000	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:32515400-32538800	Weak transcription	NHEK	skin
10	chr2:32517200-32536200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:32517400-32553200	Weak transcription	Stomach Mucosa	stomach
12	chr2:32520200-32537200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:32520600-32535600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:32520600-32537400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:32520600-32541800	Weak transcription	Brain Substantia Nigra	brain
16	chr2:32521000-32535200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:32521000-32554600	Weak transcription	Ovary	ovary
18	chr2:32521800-32552400	Weak transcription	Fetal Kidney	kidney
19	chr2:32523400-32547200	Weak transcription	NH-A	brain
20	chr2:32525000-32537400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:32525400-32548600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:32526600-32536000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:32526600-32537000	Weak transcription	HMEC	breast
24	chr2:32526600-32541800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:32526800-32548600	Weak transcription	Fetal Brain Female	brain
26	chr2:32528400-32544400	Weak transcription	NHDF-Ad	bronchial
27	chr2:32528600-32535400	Weak transcription	Esophagus	oesophagus
28	chr2:32528600-32556400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:32528800-32535400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:32528800-32535400	Weak transcription	Left Ventricle	heart
31	chr2:32528800-32535600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:32528800-32535600	Weak transcription	Fetal Lung	lung
33	chr2:32528800-32538400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:32528800-32538400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:32528800-32539400	Weak transcription	Pancreas	Pancrea
36	chr2:32528800-32547200	Weak transcription	Lung	lung
37	chr2:32528800-32547400	Weak transcription	Aorta	Aorta
38	chr2:32528800-32548000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:32528800-32548400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:32528800-32555000	Weak transcription	Gastric	stomach
41	chr2:32528800-32555800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:32528800-32555800	Weak transcription	Spleen	Spleen
43	chr2:32528800-32560800	Weak transcription	Right Ventricle	heart
44	chr2:32528800-32566200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:32529000-32537000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:32529000-32537000	Weak transcription	GM12878-XiMat	blood
47	chr2:32529000-32554000	Weak transcription	Fetal Heart	heart
48	chr2:32529200-32535400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:32529200-32535800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:32529200-32550000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links