Variant report

Variant	rs57380389
Chromosome Location	chr1:224028389-224028390
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	chr1:224006162..224007955-chr1:224027142..224029222,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10158199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10158843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10159010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1153962	1.00[EUR][1000 genomes]
rs1153966	1.00[EUR][1000 genomes]
rs12025911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12026548	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12027762	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12040996	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12047952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1222131	1.00[EUR][1000 genomes]
rs12239235	1.00[EUR][1000 genomes]
rs12239402	1.00[EUR][1000 genomes]
rs12239445	1.00[EUR][1000 genomes]
rs12239678	1.00[EUR][1000 genomes]
rs13375296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842078	1.00[EUR][1000 genomes]
rs16842173	1.00[EUR][1000 genomes]
rs16842177	1.00[EUR][1000 genomes]
rs16842201	1.00[EUR][1000 genomes]
rs16842217	1.00[EUR][1000 genomes]
rs16842234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842259	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1890119	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2230082	1.00[EUR][1000 genomes]
rs28370064	1.00[EUR][1000 genomes]
rs28370079	1.00[EUR][1000 genomes]
rs28370099	1.00[EUR][1000 genomes]
rs28370160	1.00[EUR][1000 genomes]
rs28370161	1.00[EUR][1000 genomes]
rs28370162	1.00[EUR][1000 genomes]
rs28458390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28684725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41345146	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56947789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58753599	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59433589	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59793743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59948383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59970447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61056357	1.00[EUR][1000 genomes]
rs61162360	1.00[EUR][1000 genomes]
rs6664674	1.00[EUR][1000 genomes]
rs73114413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122500	1.00[EUR][1000 genomes]
rs73125398	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73127405	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73127411	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73127438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73127450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs747811	1.00[EUR][1000 genomes]
rs7515215	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286986	1.00[EUR][1000 genomes]
rs9970756	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:224020800-224028600	Weak transcription	Placenta	Placenta
3	chr1:224020800-224031600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:224023000-224029000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:224023000-224030600	Weak transcription	Fetal Kidney	kidney
6	chr1:224023200-224031600	Weak transcription	Hela-S3	cervix
7	chr1:224024000-224031800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:224024000-224031800	Weak transcription	Thymus	Thymus
9	chr1:224024200-224031600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:224024200-224031800	Weak transcription	Adipose Nuclei	Adipose
13	chr1:224024400-224031800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:224024600-224028800	Weak transcription	Psoas Muscle	Psoas
15	chr1:224024600-224029600	Weak transcription	Pancreas	Pancrea
16	chr1:224024600-224030800	Weak transcription	Primary B cells from cord blood	blood
17	chr1:224024600-224031600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:224024600-224031800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:224024600-224031800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:224024600-224031800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:224024600-224031800	Weak transcription	Esophagus	oesophagus
22	chr1:224025200-224030000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:224025200-224030600	Weak transcription	NHEK	skin
24	chr1:224025200-224031800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:224025400-224029400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:224025600-224032200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:224025800-224029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:224025800-224029800	Weak transcription	Fetal Brain Male	brain
29	chr1:224026000-224030000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:224026000-224031600	Weak transcription	Fetal Intestine Small	intestine
31	chr1:224026200-224028600	Weak transcription	Liver	Liver
32	chr1:224026200-224029200	Weak transcription	A549	lung
33	chr1:224026200-224030000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:224026200-224031800	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:224026400-224028400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:224026400-224028600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:224026400-224028600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:224026400-224028600	Weak transcription	Ovary	ovary
39	chr1:224026400-224029200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:224026400-224029400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:224026400-224029800	Weak transcription	Brain Angular Gyrus	brain
42	chr1:224026400-224030000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:224026400-224030000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:224026400-224030000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr1:224026400-224030000	Weak transcription	Small Intestine	intestine
46	chr1:224026400-224030400	Weak transcription	Primary T cells from cord blood	blood
47	chr1:224026400-224030600	Weak transcription	HepG2	liver
48	chr1:224026400-224030600	Weak transcription	HUVEC	blood vessel
49	chr1:224026400-224031600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:224026400-224031600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links