Variant report

Variant	rs468851
Chromosome Location	chr22:29956137-29956138
allele	C/T
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	POLR2A	chr22:29955877-29956529	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29953914..29956563-chr22:29957184..29959467,2	K562	blood:
2	chr22:29949790..29952573-chr22:29954759..29957359,3	MCF-7	breast:
3	chr22:29946832..29952460-chr22:29954697..29959036,10	MCF-7	breast:
4	chr22:29949233..29951054-chr22:29955559..29957490,2	K562	blood:

Variant related genes	Relation type
THOC5	TF binding region
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2007668	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2024117	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2052023	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2079647	0.84[EUR][1000 genomes]
rs2283860	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2530661	0.83[EUR][1000 genomes]
rs2531844	0.82[EUR][1000 genomes]
rs456300	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs457765	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs465938	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs467812	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468150	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs468217	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs468221	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468902	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468986	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763294	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763295	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763296	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763302	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763304	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6006179	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs695399	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737976	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs737977	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613968	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9613976	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs468851	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs468851	NIPSNAP1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29950200-29976000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29950400-29957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr22:29950400-29965200	Weak transcription	Small Intestine	intestine
4	chr22:29950400-29976200	Weak transcription	HMEC	breast
5	chr22:29950600-29957000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr22:29950600-29958400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr22:29950600-29962200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr22:29950600-29964800	Strong transcription	Fetal Intestine Large	intestine
9	chr22:29950600-29964800	Strong transcription	Fetal Intestine Small	intestine
10	chr22:29950600-29967400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:29950600-29967600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:29950600-29968000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:29950800-29956600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr22:29950800-29958400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:29950800-29958400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr22:29950800-29958400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr22:29950800-29958600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr22:29950800-29958800	Strong transcription	Fetal Brain Female	brain
20	chr22:29950800-29959200	Weak transcription	Hela-S3	cervix
21	chr22:29950800-29959600	Weak transcription	Fetal Heart	heart
22	chr22:29950800-29959600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr22:29950800-29961600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:29950800-29966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:29950800-29966800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr22:29950800-29967000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr22:29951000-29957200	Strong transcription	NH-A	brain
29	chr22:29951000-29958200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr22:29951000-29958400	Strong transcription	Placenta	Placenta
31	chr22:29951000-29958600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr22:29951000-29958600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr22:29951000-29958600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr22:29951000-29958600	Strong transcription	Spleen	Spleen
35	chr22:29951000-29958600	Strong transcription	Osteobl	bone
36	chr22:29951000-29960000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:29951000-29962000	Strong transcription	Thymus	Thymus
38	chr22:29951000-29966600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr22:29951000-29966800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr22:29951000-29967400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr22:29951000-29967400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr22:29951000-29967600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr22:29951200-29958200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr22:29951200-29958400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:29951200-29958400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:29951200-29958400	Strong transcription	Fetal Thymus	thymus
47	chr22:29951200-29958400	Strong transcription	Dnd41	blood
48	chr22:29951200-29958600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr22:29951200-29958600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr22:29951200-29958600	Strong transcription	Brain Germinal Matrix	brain

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