Variant report

Variant	rs9608806
Chromosome Location	chr22:30095706-30095707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30091841..30093848-chr22:30094919..30097302,3	MCF-7	breast:
2	chr22:30086550..30091376-chr22:30091742..30099600,10	MCF-7	breast:
3	chr22:30094321..30096563-chr22:30160914..30162763,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1034880	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476757	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071622	0.92[AFR][1000 genomes]
rs2252472	0.92[AFR][1000 genomes]
rs2252587	0.92[AFR][1000 genomes]
rs2267150	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2267151	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283863	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283864	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2530672	0.86[AFR][1000 genomes]
rs2530673	0.81[AFR][1000 genomes]
rs2530675	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2530676	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2857639	0.92[AFR][1000 genomes]
rs2857640	0.92[AFR][1000 genomes]
rs2857641	0.93[AFR][1000 genomes]
rs2857642	0.92[AFR][1000 genomes]
rs2857645	0.88[AFR][1000 genomes]
rs2857648	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2857649	0.92[EUR][1000 genomes]
rs2857650	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857651	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5752953	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763409	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763422	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763423	0.88[EUR][1000 genomes]
rs5763431	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7291645	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737931	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	nsv529737	chr22:30060946-30109561	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv914965	chr22:30086144-30112226	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv914966	chr22:30088442-30138548	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9608806	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
2	chr22:30075400-30097400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:30076800-30096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr22:30077800-30096400	Weak transcription	Small Intestine	intestine
5	chr22:30079600-30097000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr22:30079600-30097400	Weak transcription	Hela-S3	cervix
7	chr22:30080000-30097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr22:30080200-30098800	Weak transcription	GM12878-XiMat	blood
9	chr22:30081000-30096400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr22:30081200-30096400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr22:30085800-30096200	Weak transcription	Fetal Kidney	kidney
12	chr22:30086400-30096600	Weak transcription	NHDF-Ad	bronchial
13	chr22:30086600-30098000	Weak transcription	Colon Smooth Muscle	Colon
14	chr22:30087000-30098400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:30088200-30096400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr22:30088200-30096800	Weak transcription	K562	blood
17	chr22:30088400-30096200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:30088400-30096400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:30089000-30095800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr22:30089000-30096800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr22:30089200-30096200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr22:30089600-30098200	Weak transcription	Right Atrium	heart
23	chr22:30090400-30096400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr22:30090400-30096600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr22:30090600-30097000	Weak transcription	HepG2	liver
26	chr22:30090800-30096400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr22:30090800-30097400	Weak transcription	Primary B cells from cord blood	blood
28	chr22:30091000-30095800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr22:30091400-30095800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr22:30091600-30097200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr22:30092000-30095800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr22:30092000-30095800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr22:30092000-30095800	Weak transcription	HSMMtube	muscle
34	chr22:30092000-30096000	Weak transcription	Fetal Brain Male	brain
35	chr22:30092000-30096400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:30092000-30096400	Weak transcription	Colonic Mucosa	Colon
37	chr22:30092000-30096400	Weak transcription	Right Ventricle	heart
38	chr22:30092000-30096400	Weak transcription	NHEK	skin
39	chr22:30092000-30096800	Weak transcription	Esophagus	oesophagus
40	chr22:30092000-30096800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr22:30092000-30097400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr22:30092200-30096600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr22:30092200-30096800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr22:30092400-30096400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr22:30092600-30096200	Weak transcription	Fetal Brain Female	brain
46	chr22:30092600-30096200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr22:30092600-30096800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr22:30092600-30098200	Weak transcription	Liver	Liver
49	chr22:30092800-30096800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr22:30092800-30097000	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links