Variant report

Variant	rs468902
Chromosome Location	chr22:29963508-29963509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29961562..29963537-chr22:29964937..29966766,2	MCF-7	breast:
2	chr22:29959743..29962001-chr22:29963309..29966243,2	MCF-7	breast:
3	chr22:29956204..29958172-chr22:29960992..29963868,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs2007668	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2024117	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2052023	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2079647	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2283860	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2527334	0.94[JPT][hapmap]
rs2527335	0.93[JPT][hapmap]
rs2530661	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2530662	0.94[JPT][hapmap]
rs2531844	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2857638	0.94[JPT][hapmap]
rs2857643	0.94[JPT][hapmap]
rs2857647	0.94[JPT][hapmap]
rs456300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457765	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs465938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs467812	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs468217	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468221	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468851	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468986	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763294	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763295	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5763296	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5763302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763378	0.93[JPT][hapmap]
rs6006179	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6519793	0.94[JPT][hapmap]
rs695399	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737976	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs737977	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8140060	0.87[JPT][hapmap]
rs9613968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9613976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[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
rs468902	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs468902	NIPSNAP1	cis	Artery Tibial	GTEx

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	chr22:29950600-29964800	Strong transcription	Fetal Intestine Large	intestine
5	chr22:29950600-29964800	Strong transcription	Fetal Intestine Small	intestine
6	chr22:29950600-29967400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr22:29950600-29967600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr22:29950600-29968000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:29950600-29971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:29950800-29966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:29950800-29966800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr22:29950800-29967000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr22:29950800-29976200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr22:29951000-29966600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr22:29951000-29966800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:29951000-29967400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr22:29951000-29967400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr22:29951000-29967600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr22:29951200-29966400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:29951200-29967600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr22:29951200-29971400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr22:29951600-29971600	Strong transcription	Fetal Stomach	stomach
23	chr22:29952000-29966600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr22:29952000-29976400	Weak transcription	Right Atrium	heart
25	chr22:29952800-29964800	Weak transcription	HSMMtube	muscle
26	chr22:29953400-29966200	Strong transcription	Liver	Liver
27	chr22:29955000-29976000	Weak transcription	NHEK	skin
28	chr22:29955400-29964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr22:29955400-29976000	Weak transcription	HUVEC	blood vessel
30	chr22:29957400-29976200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr22:29957600-29976200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr22:29957800-29968400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr22:29958000-29975800	Weak transcription	Stomach Mucosa	stomach
34	chr22:29958200-29964800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr22:29958400-29964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr22:29958400-29964800	Weak transcription	Adipose Nuclei	Adipose
37	chr22:29958400-29964800	Weak transcription	Placenta	Placenta
38	chr22:29958400-29964800	Weak transcription	Pancreas	Pancrea
39	chr22:29958400-29964800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr22:29958400-29964800	Weak transcription	Right Ventricle	heart
41	chr22:29958400-29964800	Weak transcription	A549	lung
42	chr22:29958400-29964800	Weak transcription	GM12878-XiMat	blood
43	chr22:29958400-29965000	Weak transcription	NHLF	lung
44	chr22:29958400-29976000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr22:29958400-29976200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr22:29958400-29976400	Weak transcription	Primary B cells from cord blood	blood
47	chr22:29958400-29976400	Weak transcription	NHDF-Ad	bronchial
48	chr22:29958600-29964800	Weak transcription	Spleen	Spleen
49	chr22:29958600-29976200	Weak transcription	HSMM	muscle
50	chr22:29959400-29963800	Strong transcription	Brain Germinal Matrix	brain

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