Variant report

Variant	rs12401336
Chromosome Location	chr1:160988944-160988945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160970990..160972886-chr1:160988444..160990539,2	MCF-7	breast:
2	chr1:160957625..160960589-chr1:160987961..160989680,2	K562	blood:
3	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
4	chr1:160988253..160990584-chr1:161134900..161137234,2	K562	blood:
5	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
6	chr1:160967150..160969611-chr1:160987527..160989808,2	K562	blood:
7	chr1:160987801..160992609-chr1:161065993..161069595,4	MCF-7	breast:
8	chr1:160986835..160990359-chr1:161086146..161091164,5	K562	blood:
9	chr1:160969730..160971940-chr1:160985751..160989711,3	MCF-7	breast:
10	chr1:160988368..160992141-chr1:161085559..161090183,5	MCF-7	breast:
11	chr1:160988517..160990791-chr1:161000780..161003550,2	K562	blood:
12	chr1:160988859..160991431-chr1:161086289..161089011,2	K562	blood:
13	chr1:160986477..160990791-chr1:161000780..161004789,4	K562	blood:
14	chr1:160987861..160992104-chr1:161101436..161104060,5	K562	blood:
15	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
16	chr1:160988315..160990144-chr1:161088244..161090577,2	MCF-7	breast:
17	chr1:160986531..160989585-chr1:160990599..160993711,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000158773	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000143224	Chromatin interaction
ENSG00000232879	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000162755	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1044478	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1062826	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1062827	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265540	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11265542	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799478	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799521	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11801586	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11805856	0.88[AMR][1000 genomes]
rs11807930	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12405782	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12408778	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12565932	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17388108	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806774	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073655	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073656	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073658	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2243427	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247459	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247596	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247671	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247790	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251597	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251728	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265243	0.81[ASN][1000 genomes]
rs2297219	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297220	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297221	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297222	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481080	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2481081	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2481083	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481084	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481085	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483145	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2774274	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2988726	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3119321	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737785	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3737787	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41267947	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41267949	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41267951	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41269993	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4339888	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55728374	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61802231	0.86[AMR][1000 genomes]
rs61803664	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61803665	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61803671	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61803672	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712854	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs812741	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869985	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160983600-160989400	Enhancers	Placenta	Placenta
2	chr1:160984200-160989400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:160984200-160989600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:160984200-160989600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:160984200-160989800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:160984400-160989000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:160984400-160989400	Weak transcription	Primary T cells from cord blood	blood
8	chr1:160984400-160989400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:160984400-160989400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:160984400-160989400	Weak transcription	Fetal Kidney	kidney
11	chr1:160984400-160989600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:160984400-160989600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:160984400-160989800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:160984400-160989800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:160984400-160989800	Weak transcription	Right Ventricle	heart
16	chr1:160984400-160990800	Weak transcription	HSMMtube	muscle
17	chr1:160984400-160991000	Weak transcription	HSMM	muscle
18	chr1:160984600-160989000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:160985600-160989400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:160986400-160989600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:160986400-160989800	Enhancers	Pancreas	Pancrea
22	chr1:160987400-160989000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:160987400-160989000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:160987400-160989400	Enhancers	Stomach Mucosa	stomach
25	chr1:160987600-160989000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:160987600-160989000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr1:160987600-160989000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:160987600-160989000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:160987600-160989000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr1:160987600-160989000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:160987600-160989000	Flanking Active TSS	K562	blood
32	chr1:160987600-160989200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr1:160987600-160989400	Enhancers	Adipose Nuclei	Adipose
34	chr1:160987600-160990200	Enhancers	Spleen	Spleen
35	chr1:160987800-160989000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:160987800-160989000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
37	chr1:160987800-160989400	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr1:160987800-160989800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:160987800-160989800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:160987800-160989800	Enhancers	Fetal Thymus	thymus
41	chr1:160987800-160990400	Weak transcription	Aorta	Aorta
42	chr1:160987800-160990600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:160987800-160990800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr1:160988000-160989000	Transcr. at gene 5' and 3'	HMEC	breast
45	chr1:160988000-160989800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:160988000-160989800	Weak transcription	Left Ventricle	heart
47	chr1:160988000-160992000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:160988200-160989000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:160988200-160989000	Enhancers	HepG2	liver
50	chr1:160988200-160989400	Flanking Active TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links