Variant report

Variant	rs62169481
Chromosome Location	chr2:148620261-148620262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:148618900..148620557-chr2:148620956..148623772,2	MCF-7	breast:
2	chr2:148599271..148602254-chr2:148619088..148621822,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121989	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1424941	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469211	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17218938	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17225402	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17225423	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17225430	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17232078	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17691284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17692648	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17741344	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17741978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17742134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17742246	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17742342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743157	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754541	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820715	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62169472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169473	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169474	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169475	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs62169477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169478	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169479	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62169480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62169482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62169483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721344	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs730356	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7560502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7595052	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7602296	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs929940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148606000-148620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:148606200-148620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:148609400-148620800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:148613000-148627400	Weak transcription	Pancreas	Pancrea
6	chr2:148613000-148640800	Weak transcription	Lung	lung
7	chr2:148613200-148625600	Weak transcription	Right Atrium	heart
8	chr2:148613200-148631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:148614400-148620400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:148614600-148621400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr2:148615400-148623200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:148615800-148621000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:148615800-148626200	Weak transcription	Ovary	ovary
14	chr2:148616200-148621000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:148616600-148620400	Weak transcription	Fetal Intestine Small	intestine
16	chr2:148616800-148636200	Weak transcription	Small Intestine	intestine
17	chr2:148617600-148620600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:148617800-148621400	Weak transcription	HUVEC	blood vessel
19	chr2:148617800-148624400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:148618000-148620600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:148618000-148620800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:148618000-148621600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:148618000-148625400	Weak transcription	Right Ventricle	heart
24	chr2:148618000-148625600	Weak transcription	HSMMtube	muscle
25	chr2:148618000-148627400	Weak transcription	Fetal Brain Male	brain
26	chr2:148618000-148627400	Weak transcription	Gastric	stomach
27	chr2:148618400-148620400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:148618400-148620400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:148618400-148620600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:148618400-148620600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:148618400-148620800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:148618400-148626800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:148618400-148627400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:148618600-148626800	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:148618600-148627000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:148619000-148621000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr2:148619200-148620800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:148619200-148621000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr2:148619200-148621000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:148619200-148621200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:148619200-148621400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:148619200-148621800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:148619400-148621200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:148619400-148621200	Enhancers	HepG2	liver
45	chr2:148619600-148621000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:148619600-148621200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:148619600-148621200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:148619600-148621600	Enhancers	Stomach Mucosa	stomach
49	chr2:148619800-148620600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:148619800-148620800	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links