Variant report

Variant	rs98069
Chromosome Location	chr22:29730625-29730626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr22:29730528-29730960	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29663885..29666768-chr22:29729647..29731238,2	MCF-7	breast:
2	chr22:29702926..29704904-chr22:29730229..29732410,2	MCF-7	breast:

Variant related genes	Relation type
SNORD125	TF binding region
AP1B1	TF binding region
ENSG00000100263	Chromatin interaction
ENSG00000185340	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11090564	0.88[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs131180	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131182	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs131189	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs140062	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140063	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140066	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs174759	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs174761	0.81[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174762	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap]
rs174764	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174765	0.94[ASN][1000 genomes]
rs174766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174767	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs174769	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs174770	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs174771	0.91[ASN][1000 genomes]
rs174775	0.86[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap]
rs2071578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072051	0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2267132	0.82[CHB][hapmap]
rs2267133	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap]
rs2283849	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283850	0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2301290	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs2301585	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519486	0.84[ASN][1000 genomes]
rs2857462	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857466	0.83[JPT][hapmap]
rs28755	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788410	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3788411	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820803	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs4820804	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752903	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs5763138	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs5763139	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763178	0.91[ASN][1000 genomes]
rs6006090	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6006098	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs715494	0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs879580	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs9537	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29707400-29740000	Weak transcription	Hela-S3	cervix
2	chr22:29711800-29733400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:29719600-29730800	Weak transcription	HMEC	breast
4	chr22:29720600-29732200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:29720600-29740000	Weak transcription	Fetal Brain Male	brain
6	chr22:29721200-29732000	Weak transcription	K562	blood
7	chr22:29721400-29738200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr22:29721400-29746800	Strong transcription	Fetal Intestine Small	intestine
9	chr22:29721800-29734400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:29721800-29739600	Strong transcription	Colonic Mucosa	Colon
11	chr22:29721800-29756800	Strong transcription	Primary T cells from cord blood	blood
12	chr22:29722000-29732400	Strong transcription	Gastric	stomach
13	chr22:29722000-29732800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr22:29722000-29739200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:29722000-29739800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr22:29722000-29747000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr22:29722000-29759200	Strong transcription	Dnd41	blood
18	chr22:29722000-29759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr22:29722200-29733000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:29722200-29737000	Strong transcription	Pancreas	Pancrea
21	chr22:29722200-29738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr22:29722200-29738000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr22:29722200-29739400	Strong transcription	Fetal Brain Female	brain
24	chr22:29722200-29741000	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr22:29722200-29755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:29722200-29756400	Strong transcription	Thymus	Thymus
27	chr22:29722200-29756600	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr22:29722200-29759800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr22:29722400-29733000	Weak transcription	Stomach Mucosa	stomach
30	chr22:29722400-29735000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr22:29722400-29736600	Weak transcription	Fetal Heart	heart
32	chr22:29722400-29739400	Strong transcription	Brain Germinal Matrix	brain
33	chr22:29722400-29740400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr22:29722400-29740400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr22:29722400-29756800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr22:29722400-29758400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr22:29722600-29732400	Strong transcription	Left Ventricle	heart
38	chr22:29722600-29738000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr22:29722600-29738400	Strong transcription	Aorta	Aorta
40	chr22:29722600-29739800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr22:29722600-29751200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr22:29722600-29753200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr22:29722600-29755400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr22:29722600-29756000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr22:29722600-29757200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr22:29722600-29758000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr22:29722600-29758800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr22:29723000-29739400	Strong transcription	Fetal Thymus	thymus
49	chr22:29723000-29758800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr22:29723000-29765000	Strong transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links