Variant report

Variant	rs2345639
Chromosome Location	chr2:153031113-153031114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153030097..153032269-chr2:153191350..153193391,2	MCF-7	breast:
2	chr2:153020830..153022927-chr2:153028823..153031292,2	MCF-7	breast:
3	chr2:153030659..153033731-chr2:153574261..153576507,5	MCF-7	breast:
4	chr2:153029944..153031491-chr2:153562349..153565101,2	K562	blood:
5	chr2:153030783..153033861-chr2:153572629..153575835,5	MCF-7	breast:
6	chr2:153030399..153031965-chr2:153038673..153040323,2	K562	blood:
7	chr2:153031056..153034207-chr2:153571978..153575897,4	K562	blood:

Variant related genes	Relation type
ENSG00000157827	Chromatin interaction
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10200655	0.86[CHB][hapmap]
rs10427181	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10803936	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10803938	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10930910	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10930913	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10930916	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10930958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12328066	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12465272	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs12466663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467850	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12474703	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12617139	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617696	0.86[CHB][hapmap]
rs12693269	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995261	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs13000396	1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13009432	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs13027217	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1401778	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17326047	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17326118	1.00[JPT][hapmap]
rs17326628	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17326677	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17398329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17398559	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17398585	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1879136	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1962276	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345638	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2345648	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345650	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2345895	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2345896	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2345898	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2881245	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35195960	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35594562	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35820971	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3768650	0.86[CHB][hapmap]
rs3820702	0.86[CHB][hapmap]
rs4274558	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4305274	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4664078	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4664536	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55677048	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55837285	0.90[EUR][1000 genomes]
rs56018021	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56118729	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56127412	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56888625	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57542496	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62174961	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62176480	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62176518	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62176559	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177360	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62177369	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6433779	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6650771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6730115	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6731625	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6732917	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6738680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6740224	0.86[CHB][hapmap]
rs6741737	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6742259	1.00[CEU][hapmap]
rs6754105	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72857747	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72864757	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557426	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7579071	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7582231	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7592014	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7600282	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7603232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv459740	chr2:152986041-153045036	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv583316	chr2:152986041-153045036	Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv3693434	chr2:152998467-153208713	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153022200-153031400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:153022800-153031200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:153022800-153031200	Weak transcription	Gastric	stomach
4	chr2:153022800-153031200	Weak transcription	Left Ventricle	heart
5	chr2:153027600-153031200	Weak transcription	Lung	lung
6	chr2:153028200-153031200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:153028400-153031400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:153029200-153031200	Weak transcription	Placenta	Placenta
9	chr2:153029200-153031200	Weak transcription	Ovary	ovary
10	chr2:153029200-153031200	Weak transcription	Pancreas	Pancrea
11	chr2:153029400-153031400	Weak transcription	Spleen	Spleen
12	chr2:153030000-153031200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr2:153030000-153031400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:153030200-153031200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:153030200-153031200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:153030200-153033200	Active TSS	Psoas Muscle	Psoas
17	chr2:153030200-153033200	Active TSS	GM12878-XiMat	blood
18	chr2:153030400-153031200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:153030400-153031200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:153030400-153031200	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:153030400-153031200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:153030400-153031200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:153030400-153031200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:153030400-153031200	Enhancers	Brain Angular Gyrus	brain
25	chr2:153030400-153031200	Enhancers	Brain Substantia Nigra	brain
26	chr2:153030400-153031200	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr2:153030400-153031200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:153030400-153031200	Flanking Active TSS	HepG2	liver
29	chr2:153030400-153031400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:153030400-153031400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:153030400-153031400	Flanking Active TSS	Dnd41	blood
32	chr2:153030400-153031600	Flanking Active TSS	Liver	Liver
33	chr2:153030400-153033200	Active TSS	Right Atrium	heart
34	chr2:153030400-153033400	Active TSS	HSMMtube	muscle
35	chr2:153030400-153033400	Active TSS	NHDF-Ad	bronchial
36	chr2:153030600-153031400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:153030600-153031400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:153030600-153031400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:153030600-153031400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:153030600-153031400	Weak transcription	Esophagus	oesophagus
41	chr2:153030600-153031400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:153030600-153032800	Active TSS	NH-A	brain
43	chr2:153030600-153033200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:153030600-153033200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:153030600-153033200	Active TSS	Fetal Intestine Large	intestine
46	chr2:153030800-153031200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr2:153030800-153031200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr2:153030800-153031200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:153030800-153031200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:153030800-153031200	Flanking Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links