Variant report

Variant	rs467669
Chromosome Location	chr22:29965168-29965169
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29964781..29966477-chr22:29968407..29970909,2	K562	blood:
2	chr22:29959743..29962001-chr22:29963309..29966243,2	MCF-7	breast:
3	chr22:29961562..29963537-chr22:29964937..29966766,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1009147	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs105268	1.00[JPT][hapmap]
rs11090576	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs165602	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs165607	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs165624	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs165633	1.00[JPT][hapmap]
rs165649	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs165697	0.80[AMR][1000 genomes]
rs165734	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs165821	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs165823	0.80[AMR][1000 genomes]
rs165853	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs165899	0.88[AMR][1000 genomes]
rs17460259	0.84[AFR][1000 genomes]
rs174649	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs174718	1.00[JPT][hapmap]
rs1800540	0.81[ASN][1000 genomes]
rs2008880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2530660	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2857634	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs424541	0.80[AMR][1000 genomes]
rs457930	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs465736	1.00[JPT][hapmap]
rs467768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468563	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469189	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4823046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4823048	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5752917	1.00[JPT][hapmap]
rs5763315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763347	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763348	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6006219	1.00[JPT][hapmap]
rs695776	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73159014	0.96[ASN][1000 genomes]
rs737979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625852	0.82[CHB][hapmap];1.00[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs467669	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr22:29950400-29965200	Weak transcription	Small Intestine	intestine
3	chr22:29950400-29976200	Weak transcription	HMEC	breast
4	chr22:29950600-29967400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:29950600-29967600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr22:29950600-29968000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29950800-29966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:29950800-29966800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr22:29950800-29967000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr22:29951000-29966600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr22:29951000-29966800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:29951000-29967400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr22:29951000-29967400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr22:29951000-29967600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr22:29951200-29966400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:29951200-29967600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr22:29951200-29971400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr22:29951600-29971600	Strong transcription	Fetal Stomach	stomach
21	chr22:29952000-29966600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:29952000-29976400	Weak transcription	Right Atrium	heart
23	chr22:29953400-29966200	Strong transcription	Liver	Liver
24	chr22:29955000-29976000	Weak transcription	NHEK	skin
25	chr22:29955400-29976000	Weak transcription	HUVEC	blood vessel
26	chr22:29957400-29976200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr22:29957600-29976200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr22:29957800-29968400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr22:29958000-29975800	Weak transcription	Stomach Mucosa	stomach
30	chr22:29958400-29976000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr22:29958400-29976200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr22:29958400-29976400	Weak transcription	Primary B cells from cord blood	blood
33	chr22:29958400-29976400	Weak transcription	NHDF-Ad	bronchial
34	chr22:29958600-29976200	Weak transcription	HSMM	muscle
35	chr22:29959400-29966400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr22:29959400-29966600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr22:29959400-29966600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr22:29959400-29967000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr22:29959400-29967000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:29959400-29967200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr22:29959400-29967200	Strong transcription	Fetal Muscle Leg	muscle
42	chr22:29959400-29967600	Strong transcription	Primary T cells from cord blood	blood
43	chr22:29959600-29967000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:29959600-29967000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr22:29959600-29967600	Strong transcription	Fetal Brain Female	brain
46	chr22:29959800-29967200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:29959800-29967600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:29960000-29966600	Strong transcription	Fetal Thymus	thymus
49	chr22:29960800-29966800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr22:29961000-29967800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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