Variant report

Variant	rs28541979
Chromosome Location	chr22:29438785-29438786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29248944..29251170-chr22:29435947..29438791,2	MCF-7	breast:
2	chr22:29436637..29439256-chr22:29468690..29471478,2	MCF-7	breast:
3	chr22:29436800..29439536-chr22:29439547..29442052,2	K562	blood:
4	chr22:29195509..29198134-chr22:29437512..29441446,4	K562	blood:
5	chr22:29195462..29200064-chr22:29436514..29439223,5	MCF-7	breast:
6	chr22:29437866..29439720-chr22:29487851..29489925,2	MCF-7	breast:
7	chr22:29436460..29439991-chr22:29442261..29446083,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000183762	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12484832	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12485244	0.86[EUR][1000 genomes]
rs132565	0.88[ASN][1000 genomes]
rs1883197	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1977047	0.84[EUR][1000 genomes]
rs1983553	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072774	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2103544	0.90[EUR][1000 genomes]
rs2347789	0.81[EUR][1000 genomes]
rs2347790	0.80[EUR][1000 genomes]
rs4140643	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4333023	0.81[EUR][1000 genomes]
rs4404379	0.83[EUR][1000 genomes]
rs4580479	0.84[ASN][1000 genomes]
rs469994	0.88[ASN][1000 genomes]
rs4820794	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4823002	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4823003	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4823005	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5997430	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs5997431	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs5997432	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997433	0.89[EUR][1000 genomes]
rs5997434	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs5997435	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005954	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6005955	0.83[EUR][1000 genomes]
rs6005956	0.83[EUR][1000 genomes]
rs6005958	0.82[EUR][1000 genomes]
rs6005959	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6005964	0.81[EUR][1000 genomes]
rs6005965	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6005967	0.89[EUR][1000 genomes]
rs713834	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727892	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7284304	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7287517	0.90[EUR][1000 genomes]
rs7290304	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs738246	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8137254	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8137499	0.88[ASN][1000 genomes]
rs8142591	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs874915	0.85[EUR][1000 genomes]
rs874916	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs874917	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608719	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9608721	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613771	0.82[EUR][1000 genomes]
rs9613776	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9613777	0.87[EUR][1000 genomes]
rs9613784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613785	0.89[EUR][1000 genomes];0.84[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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29427400-29448400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29427800-29451400	Weak transcription	Psoas Muscle	Psoas
3	chr22:29428000-29441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:29428600-29440400	Weak transcription	Esophagus	oesophagus
5	chr22:29428600-29440800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:29428800-29443600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr22:29429000-29440600	Weak transcription	Colonic Mucosa	Colon
8	chr22:29429000-29444000	Weak transcription	Right Ventricle	heart
9	chr22:29429800-29439400	Weak transcription	Aorta	Aorta
10	chr22:29433800-29440600	Weak transcription	Lung	lung
11	chr22:29434000-29439200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:29434000-29439200	Weak transcription	Pancreas	Pancrea
13	chr22:29435400-29439200	Weak transcription	Fetal Muscle Leg	muscle
14	chr22:29435400-29440000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr22:29435400-29440400	Weak transcription	Gastric	stomach
16	chr22:29436400-29438800	Enhancers	Osteobl	bone
17	chr22:29436400-29439200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr22:29436400-29440800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr22:29436600-29439200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29436600-29439600	Weak transcription	Left Ventricle	heart
21	chr22:29436600-29440000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr22:29436800-29439200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr22:29436800-29439400	Weak transcription	Placenta	Placenta
24	chr22:29436800-29441200	Genic enhancers	HepG2	liver
25	chr22:29436800-29442600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:29436800-29443800	Weak transcription	Hela-S3	cervix
27	chr22:29436800-29445600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr22:29437000-29439000	Weak transcription	Fetal Intestine Large	intestine
29	chr22:29437200-29439000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr22:29437200-29439200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr22:29437200-29439200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr22:29437200-29439200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr22:29437200-29439400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr22:29437200-29439400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:29437200-29439400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr22:29437200-29439400	Weak transcription	NHEK	skin
37	chr22:29437200-29439600	Weak transcription	Fetal Kidney	kidney
38	chr22:29437200-29440000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr22:29437200-29440000	Weak transcription	Ovary	ovary
40	chr22:29437200-29440000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr22:29437200-29440400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr22:29437200-29440400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr22:29437200-29440600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr22:29437200-29440600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr22:29437200-29441400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr22:29437200-29442200	Weak transcription	Small Intestine	intestine
47	chr22:29437200-29443000	Weak transcription	K562	blood
48	chr22:29437200-29443200	Weak transcription	Brain Angular Gyrus	brain
49	chr22:29437200-29443800	Weak transcription	Fetal Heart	heart
50	chr22:29437200-29450800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links