Variant report

Variant	rs12622083
Chromosome Location	chr2:189935693-189935694
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189929773..189932181-chr2:189934301..189936938,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10178611	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10178886	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181597	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194682	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10195184	0.84[ASN][1000 genomes]
rs11686253	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11690723	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12693526	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693527	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12693528	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12989558	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13008197	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13391332	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13401377	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667259	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6414121	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434310	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434311	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434315	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434316	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434317	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434318	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434321	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434323	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738371	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7420511	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421040	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7421525	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7423808	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7423973	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7424137	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7424790	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7426169	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7557945	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562299	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7568732	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602447	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7606293	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv3074	chr2:189931263-189976124	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr2:189895200-189940800	Strong transcription	HSMM	muscle
2	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
4	chr2:189897000-189949000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:189898400-189938200	Weak transcription	HMEC	breast
6	chr2:189899000-189939200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:189901200-189947400	Weak transcription	Fetal Brain Male	brain
9	chr2:189902600-189937000	Strong transcription	NH-A	brain
10	chr2:189904000-189938200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:189904400-189951000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:189909200-189936200	Weak transcription	Small Intestine	intestine
13	chr2:189912400-189961600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:189914400-189937000	Strong transcription	Adipose Nuclei	Adipose
15	chr2:189914800-189946800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:189915000-189950600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:189915400-189938200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:189915400-189951000	Strong transcription	Osteobl	bone
19	chr2:189916200-189947600	Weak transcription	Spleen	Spleen
20	chr2:189922000-189938000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:189922800-189980800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:189925600-189940600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:189928200-189940800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:189929400-189941000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:189929600-189951400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:189931200-189941200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:189931400-189937000	Strong transcription	NHDF-Ad	bronchial
28	chr2:189931400-189940600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:189932400-189937000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr2:189932600-189936600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:189932600-189937000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:189933000-189938600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:189933000-189940600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:189933000-189941000	Weak transcription	Ovary	ovary
35	chr2:189933000-189960400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:189933000-189980200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:189933200-189946800	Weak transcription	Fetal Kidney	kidney
38	chr2:189933800-189939000	Weak transcription	HUVEC	blood vessel
39	chr2:189933800-189941200	Weak transcription	Aorta	Aorta
40	chr2:189933800-189947400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:189933800-189947400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:189933800-189957800	Weak transcription	Fetal Intestine Small	intestine
43	chr2:189935000-189936600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:189935000-189945800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:189935000-189946000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:189935200-189936400	Genic enhancers	Colon Smooth Muscle	Colon
47	chr2:189935200-189936600	Strong transcription	Liver	Liver
48	chr2:189935200-189938000	Strong transcription	HSMMtube	muscle
49	chr2:189935200-189947200	Strong transcription	A549	lung
50	chr2:189935400-189936000	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links