Variant report

Variant	rs5752790
Chromosome Location	chr22:29152965-29152966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29135896..29138704-chr22:29152370..29155070,2	MCF-7	breast:
2	chr22:29151815..29154169-chr22:29184646..29186865,2	MCF-7	breast:
3	chr22:29137252..29140773-chr22:29152307..29154305,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1222	0.88[EUR][1000 genomes]
rs13056546	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16987024	0.86[EUR][1000 genomes]
rs16987027	0.86[EUR][1000 genomes]
rs2235431	0.90[EUR][1000 genomes]
rs2236141	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267131	0.88[EUR][1000 genomes]
rs2269578	0.86[EUR][1000 genomes]
rs2301428	0.86[EUR][1000 genomes]
rs28458474	0.86[EUR][1000 genomes]
rs2881634	0.85[EUR][1000 genomes]
rs28846498	0.86[ASN][1000 genomes]
rs34298044	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34573837	0.92[EUR][1000 genomes]
rs34718288	0.88[EUR][1000 genomes]
rs34751572	0.92[EUR][1000 genomes]
rs34887403	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35017742	0.86[EUR][1000 genomes]
rs35829597	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35905502	0.92[EUR][1000 genomes]
rs36112964	0.90[EUR][1000 genomes]
rs5752794	0.91[EUR][1000 genomes]
rs5752796	0.87[EUR][1000 genomes]
rs5752802	0.86[EUR][1000 genomes]
rs5752803	0.86[EUR][1000 genomes]
rs5752806	0.86[EUR][1000 genomes]
rs5752811	0.85[EUR][1000 genomes]
rs5752816	0.85[EUR][1000 genomes]
rs5762758	0.87[ASN][1000 genomes]
rs5762763	0.94[ASN][1000 genomes]
rs5762764	0.95[ASN][1000 genomes]
rs5762765	0.95[ASN][1000 genomes]
rs5762767	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762774	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762794	0.88[EUR][1000 genomes]
rs5762809	0.81[EUR][1000 genomes]
rs5762812	0.86[EUR][1000 genomes]
rs5762814	0.86[EUR][1000 genomes]
rs5762816	0.86[EUR][1000 genomes]
rs5762817	0.86[EUR][1000 genomes]
rs5762818	0.86[EUR][1000 genomes]
rs5762819	0.86[EUR][1000 genomes]
rs5762820	0.86[EUR][1000 genomes]
rs5762821	0.86[EUR][1000 genomes]
rs5762823	0.86[EUR][1000 genomes]
rs60468718	0.85[EUR][1000 genomes]
rs66471734	0.86[EUR][1000 genomes]
rs71327317	0.85[EUR][1000 genomes]
rs73170633	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8184945	0.94[ASN][1000 genomes]
rs8184986	0.85[EUR][1000 genomes]
rs9613666	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	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
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29139200-29153800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:29139400-29156400	Weak transcription	Stomach Mucosa	stomach
3	chr22:29139800-29156000	Weak transcription	HMEC	breast
4	chr22:29140800-29155800	Weak transcription	Fetal Brain Female	brain
5	chr22:29141000-29153200	Weak transcription	Aorta	Aorta
6	chr22:29141200-29156400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:29143400-29156600	Weak transcription	Brain Substantia Nigra	brain
8	chr22:29143600-29154000	Weak transcription	Thymus	Thymus
9	chr22:29143600-29155600	Weak transcription	Gastric	stomach
10	chr22:29143600-29160000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr22:29143800-29153600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr22:29143800-29155600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:29143800-29156000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr22:29143800-29156400	Weak transcription	Brain Angular Gyrus	brain
15	chr22:29144000-29153400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr22:29144400-29156200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr22:29144400-29156200	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:29144400-29156200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr22:29144600-29155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr22:29144600-29155800	Weak transcription	Brain Germinal Matrix	brain
21	chr22:29144800-29154600	Weak transcription	Right Atrium	heart
22	chr22:29145200-29154800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:29145400-29154800	Weak transcription	Left Ventricle	heart
24	chr22:29145400-29155400	Weak transcription	Colon Smooth Muscle	Colon
25	chr22:29145400-29157200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr22:29145600-29155400	Weak transcription	HSMM	muscle
27	chr22:29145600-29155600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr22:29145600-29155600	Weak transcription	HSMMtube	muscle
29	chr22:29145800-29153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr22:29145800-29153800	Weak transcription	Fetal Thymus	thymus
31	chr22:29145800-29155800	Weak transcription	Ovary	ovary
32	chr22:29145800-29156200	Weak transcription	Spleen	Spleen
33	chr22:29145800-29156600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr22:29146000-29155400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr22:29146000-29155400	Weak transcription	HepG2	liver
37	chr22:29146000-29155600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr22:29146000-29155600	Weak transcription	Colonic Mucosa	Colon
39	chr22:29146000-29155800	Weak transcription	Brain Anterior Caudate	brain
40	chr22:29146000-29155800	Weak transcription	GM12878-XiMat	blood
41	chr22:29146000-29156400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr22:29146000-29156600	Weak transcription	Adipose Nuclei	Adipose
43	chr22:29146600-29156200	Weak transcription	Primary B cells from cord blood	blood
44	chr22:29146800-29156600	Weak transcription	Primary T cells from cord blood	blood
45	chr22:29146800-29156600	Weak transcription	Fetal Intestine Large	intestine
46	chr22:29147200-29153600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr22:29147200-29155800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr22:29147400-29153400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr22:29147400-29155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr22:29147400-29156000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links