Variant report

Variant	rs12028643
Chromosome Location	chr1:179266615-179266616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179262971..179265535-chr1:179265690..179267660,2	K562	blood:
2	chr1:179264767..179267490-chr1:179269682..179272613,2	K562	blood:
3	chr1:179264612..179267610-chr1:179271522..179273939,3	MCF-7	breast:
4	chr1:179266326..179267837-chr1:179289291..179292001,2	MCF-7	breast:
5	chr1:179262948..179264488-chr1:179266065..179267615,2	K562	blood:

Variant related genes	Relation type
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12022539	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026030	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12031894	0.99[EUR][1000 genomes]
rs12035050	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12039884	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12044039	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12045521	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12049122	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049237	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12402165	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12404921	0.99[EUR][1000 genomes]
rs12408349	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12408668	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1475798	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16853917	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16853936	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2068234	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2152317	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2636266	0.81[EUR][1000 genomes]
rs2636289	0.82[EUR][1000 genomes]
rs2793804	0.82[EUR][1000 genomes]
rs2793805	0.82[EUR][1000 genomes]
rs2793807	0.82[EUR][1000 genomes]
rs2793808	0.82[EUR][1000 genomes]
rs2816179	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2816180	0.88[EUR][1000 genomes]
rs3753524	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs380951	0.87[EUR][1000 genomes]
rs413881	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs425858	0.87[EUR][1000 genomes]
rs4478776	0.87[EUR][1000 genomes]
rs58284152	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58948941	0.94[EUR][1000 genomes]
rs59777301	0.93[EUR][1000 genomes]
rs60595009	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61821690	0.82[EUR][1000 genomes]
rs61821735	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61821737	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61821738	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61821739	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61821740	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61824363	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61824364	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61824365	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61824368	0.95[EUR][1000 genomes]
rs61824371	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61824388	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61824389	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6675772	0.99[EUR][1000 genomes]
rs6694339	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7414502	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179263800-179268400	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:179263800-179304600	Weak transcription	Lung	lung
4	chr1:179263800-179306400	Weak transcription	Gastric	stomach
5	chr1:179264000-179266800	Enhancers	Placenta	Placenta
6	chr1:179264000-179271400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:179264000-179279600	Weak transcription	Fetal Brain Male	brain
8	chr1:179264200-179290200	Weak transcription	Aorta	Aorta
9	chr1:179264400-179267400	Weak transcription	Spleen	Spleen
10	chr1:179264400-179267600	Weak transcription	Fetal Thymus	thymus
11	chr1:179264400-179271400	Weak transcription	Left Ventricle	heart
12	chr1:179264600-179267800	Weak transcription	A549	lung
13	chr1:179264600-179268000	Weak transcription	Thymus	Thymus
14	chr1:179264600-179268400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:179264600-179271400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:179264600-179271400	Weak transcription	Fetal Stomach	stomach
17	chr1:179264600-179271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:179264600-179271600	Weak transcription	Psoas Muscle	Psoas
19	chr1:179264600-179271600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:179264600-179272000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:179264600-179272800	Weak transcription	Fetal Lung	lung
22	chr1:179264600-179273400	Weak transcription	Fetal Intestine Small	intestine
23	chr1:179264600-179273400	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:179264600-179274200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:179264600-179275000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:179264600-179278600	Weak transcription	Colonic Mucosa	Colon
27	chr1:179264600-179281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:179264600-179292000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
30	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
31	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
32	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:179264800-179266800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:179264800-179267800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:179264800-179267800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:179264800-179268000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:179264800-179268000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:179264800-179268200	Enhancers	Primary T cells from cord blood	blood
39	chr1:179264800-179270400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:179264800-179271400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:179264800-179271400	Weak transcription	Fetal Intestine Large	intestine
42	chr1:179264800-179271600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:179264800-179271600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:179264800-179271600	Weak transcription	HMEC	breast
45	chr1:179264800-179271800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:179264800-179271800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:179264800-179272000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:179264800-179272000	Weak transcription	Brain Anterior Caudate	brain
49	chr1:179264800-179272000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:179264800-179272000	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links