Variant report

Variant	rs340332
Chromosome Location	chr2:179915438-179915439
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084229	0.89[JPT][hapmap]
rs10164707	0.90[JPT][hapmap]
rs10164814	0.88[JPT][hapmap]
rs10181464	0.90[JPT][hapmap]
rs10188759	0.90[JPT][hapmap]
rs10208593	0.89[JPT][hapmap]
rs10439300	1.00[JPT][hapmap]
rs10803924	1.00[JPT][hapmap]
rs10930852	0.87[ASN][1000 genomes]
rs10930855	0.89[JPT][hapmap]
rs10930857	0.86[JPT][hapmap]
rs12621115	0.90[JPT][hapmap]
rs12693175	0.89[JPT][hapmap]
rs12693179	0.90[JPT][hapmap]
rs12987285	0.90[JPT][hapmap]
rs13029576	0.88[JPT][hapmap]
rs13382185	0.90[JPT][hapmap]
rs13396334	0.89[JPT][hapmap]
rs13404037	0.89[JPT][hapmap]
rs1354385	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173110	0.87[ASN][1000 genomes]
rs17363260	0.89[JPT][hapmap]
rs2009639	0.94[AMR][1000 genomes]
rs2289993	0.89[JPT][hapmap]
rs2289994	0.89[JPT][hapmap]
rs2592564	0.95[ASN][1000 genomes]
rs2655158	0.95[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs340321	0.92[ASN][1000 genomes]
rs340326	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340328	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340329	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs340330	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340338	0.95[ASN][1000 genomes]
rs340349	0.90[ASN][1000 genomes]
rs340350	0.90[ASN][1000 genomes]
rs4893863	0.95[ASN][1000 genomes]
rs6433746	0.95[ASN][1000 genomes]
rs7558039	0.95[ASN][1000 genomes]
rs7598203	0.95[ASN][1000 genomes]
rs7601366	0.89[JPT][hapmap]
rs924801	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv875464	chr2:179843612-179939493	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875465	chr2:179843612-179966804	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv508184	chr2:179896384-179965419	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179909400-179916000	Weak transcription	Spleen	Spleen
2	chr2:179909600-179916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:179910800-179915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:179912600-179915600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:179912600-179915600	Active TSS	HSMMtube	muscle
6	chr2:179912600-179916200	Enhancers	Fetal Kidney	kidney
7	chr2:179912800-179916000	Active TSS	Fetal Muscle Trunk	muscle
8	chr2:179913400-179916400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:179913400-179916400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:179913600-179917000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:179913800-179916200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:179913800-179916200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:179913800-179916200	Enhancers	Fetal Lung	lung
14	chr2:179914400-179915800	Enhancers	HepG2	liver
15	chr2:179914600-179915600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr2:179914600-179916000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:179914600-179916000	Enhancers	Colon Smooth Muscle	Colon
18	chr2:179914600-179916000	Weak transcription	Placenta	Placenta
19	chr2:179914600-179916200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:179914600-179916400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr2:179914800-179915600	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr2:179914800-179915800	Weak transcription	Liver	Liver
23	chr2:179914800-179915800	Weak transcription	Pancreas	Pancrea
24	chr2:179914800-179915800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:179914800-179916000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:179914800-179916000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:179914800-179916000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:179914800-179916000	Weak transcription	Left Ventricle	heart
29	chr2:179914800-179916200	Enhancers	Fetal Intestine Small	intestine
30	chr2:179914800-179916200	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:179914800-179917000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:179915000-179915600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr2:179915000-179915600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:179915000-179915600	Active TSS	Fetal Muscle Leg	muscle
35	chr2:179915000-179916000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:179915000-179916200	Enhancers	Adipose Nuclei	Adipose
37	chr2:179915000-179916400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr2:179915000-179916400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:179915000-179916400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:179915000-179916400	Enhancers	Fetal Intestine Large	intestine
41	chr2:179915000-179916400	Enhancers	HSMM	muscle
42	chr2:179915200-179915600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:179915200-179915600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:179915200-179915600	Enhancers	Primary B cells from cord blood	blood
45	chr2:179915200-179915600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr2:179915200-179915600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr2:179915200-179915600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr2:179915200-179915600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:179915200-179915800	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr2:179915200-179915800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links