Variant report

Variant	rs5997535
Chromosome Location	chr22:30225620-30225621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30221897..30227952-chr22:30230604..30235599,8	MCF-7	breast:
2	chr22:30224439..30228420-chr22:30233600..30235751,3	K562	blood:
3	chr22:30218166..30221158-chr22:30224343..30226322,2	K562	blood:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1138120	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131293	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs131295	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs131301	0.90[ASN][1000 genomes]
rs140095	0.81[AMR][1000 genomes]
rs140145	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140147	0.87[AMR][1000 genomes]
rs140149	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140150	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17711377	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057882	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2074706	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074707	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2079338	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301402	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs249398	0.93[ASN][1000 genomes]
rs28749829	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36574	0.89[ASN][1000 genomes]
rs36576	0.93[ASN][1000 genomes]
rs3958027	0.81[AMR][1000 genomes]
rs5752961	0.92[ASN][1000 genomes]
rs5752964	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763512	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997529	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997530	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997549	0.81[AMR][1000 genomes]
rs6006274	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006288	0.81[AMR][1000 genomes]
rs713656	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs713657	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs740041	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs81800	0.92[ASN][1000 genomes]
rs9306465	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9614055	0.92[ASN][1000 genomes]
rs9614077	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5997535	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
3	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
4	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
9	chr22:30208800-30231200	Strong transcription	Lung	lung
10	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30209000-30227600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:30213600-30226000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr22:30215000-30230800	Strong transcription	Fetal Brain Female	brain
15	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:30216400-30226200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:30218000-30230600	Strong transcription	Fetal Thymus	thymus
18	chr22:30218000-30231000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr22:30218200-30232200	Strong transcription	Fetal Intestine Small	intestine
20	chr22:30218400-30225800	Weak transcription	Brain Angular Gyrus	brain
21	chr22:30218400-30233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr22:30218600-30226000	Strong transcription	Liver	Liver
23	chr22:30218600-30230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr22:30218600-30233400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr22:30219000-30232000	Weak transcription	Fetal Brain Male	brain
26	chr22:30219600-30226000	Weak transcription	A549	lung
27	chr22:30219600-30233400	Weak transcription	Fetal Kidney	kidney
28	chr22:30220000-30231600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr22:30220600-30227200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr22:30221400-30226000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:30221400-30226600	Weak transcription	HUVEC	blood vessel
32	chr22:30221400-30227400	Weak transcription	Brain Substantia Nigra	brain
33	chr22:30221400-30233400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr22:30221600-30225800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:30221600-30225800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr22:30221600-30225800	Weak transcription	HepG2	liver
37	chr22:30221600-30227200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr22:30221600-30227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr22:30221600-30227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr22:30221600-30233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:30221800-30225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr22:30221800-30226000	Weak transcription	Aorta	Aorta
43	chr22:30221800-30226000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr22:30221800-30226000	Weak transcription	Gastric	stomach
45	chr22:30221800-30226000	Weak transcription	Right Ventricle	heart
46	chr22:30221800-30226600	Weak transcription	Osteobl	bone
47	chr22:30221800-30227000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr22:30221800-30227200	Weak transcription	HSMMtube	muscle
49	chr22:30221800-30227600	Weak transcription	NHDF-Ad	bronchial
50	chr22:30221800-30229400	Weak transcription	Colonic Mucosa	Colon

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