Variant report

Variant	rs17460259
Chromosome Location	chr22:30026279-30026280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30019261..30020777-chr22:30025452..30026983,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1009147	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11090576	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17462054	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1800540	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1970776	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2079339	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2079648	0.86[AMR][1000 genomes]
rs2530660	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2857634	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs457930	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs467669	0.84[AFR][1000 genomes]
rs467768	0.84[AFR][1000 genomes]
rs468563	0.84[AFR][1000 genomes]
rs4823048	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5763347	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5763348	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5997506	0.88[EUR][1000 genomes]
rs6006219	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6006225	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73390944	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8135737	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9625852	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][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	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
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
4	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17460259	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:30014800-30032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:30015400-30026400	Weak transcription	Brain Anterior Caudate	brain
6	chr22:30018000-30026400	Weak transcription	Right Atrium	heart
7	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:30018400-30033400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr22:30019600-30026800	Enhancers	Dnd41	blood
10	chr22:30019600-30029400	Weak transcription	Esophagus	oesophagus
11	chr22:30019800-30033800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr22:30020000-30026400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr22:30020200-30029400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr22:30020200-30033200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr22:30020200-30033600	Weak transcription	GM12878-XiMat	blood
16	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
17	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
18	chr22:30020400-30032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr22:30020400-30033400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr22:30020600-30026400	Weak transcription	Right Ventricle	heart
21	chr22:30020600-30028200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr22:30020600-30029200	Weak transcription	Thymus	Thymus
23	chr22:30020600-30032800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr22:30020800-30029200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
26	chr22:30021200-30026400	Weak transcription	Left Ventricle	heart
27	chr22:30021200-30026400	Weak transcription	Spleen	Spleen
28	chr22:30021200-30026600	Weak transcription	Lung	lung
29	chr22:30021200-30029400	Weak transcription	Fetal Muscle Leg	muscle
30	chr22:30021200-30033200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr22:30021800-30029200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:30021800-30032800	Weak transcription	Liver	Liver
33	chr22:30021800-30041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr22:30022000-30028400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:30022000-30028400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr22:30022000-30033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr22:30022000-30037200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr22:30022000-30038400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr22:30022200-30028600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr22:30022200-30029200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr22:30022200-30029400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr22:30022400-30029800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr22:30022400-30032800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr22:30022600-30026400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr22:30022600-30027200	Weak transcription	Placenta	Placenta
47	chr22:30022800-30027400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:30022800-30029200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr22:30022800-30034000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr22:30023000-30037400	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links