Variant report

Variant	rs5763422
Chromosome Location	chr22:30084976-30084977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30082647..30084223-chr22:30084382..30086016,2	K562	blood:
2	chr22:30050125..30052733-chr22:30083134..30085567,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1034880	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1476757	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071622	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2245185	0.83[ASN][1000 genomes]
rs2245415	0.83[ASN][1000 genomes]
rs2252472	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2252587	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2267150	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267151	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283863	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283864	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527337	0.83[ASN][1000 genomes]
rs2530667	0.84[ASN][1000 genomes]
rs2530668	0.83[ASN][1000 genomes]
rs2530669	0.83[ASN][1000 genomes]
rs2530670	0.83[ASN][1000 genomes]
rs2530672	0.92[AFR][1000 genomes]
rs2530673	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2530675	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2530676	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2531850	0.83[ASN][1000 genomes]
rs2857637	0.83[ASN][1000 genomes]
rs2857639	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2857640	0.92[AFR][1000 genomes]
rs2857641	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2857642	0.92[AFR][1000 genomes]
rs2857645	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2857648	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857649	0.96[EUR][1000 genomes]
rs2857650	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2857651	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752953	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763409	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763423	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763431	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7291645	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737931	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608806	0.93[AFR][1000 genomes];0.93[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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763422	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
3	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr22:30051000-30085400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr22:30053400-30087400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
8	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr22:30057800-30085600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr22:30057800-30086000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr22:30060200-30093600	Strong transcription	Fetal Thymus	thymus
12	chr22:30063400-30085000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr22:30063400-30094600	Strong transcription	Primary T cells from cord blood	blood
14	chr22:30065200-30085200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:30068000-30085600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:30072800-30088200	Weak transcription	Right Atrium	heart
17	chr22:30073200-30085200	Weak transcription	Fetal Brain Male	brain
18	chr22:30073800-30085800	Weak transcription	Psoas Muscle	Psoas
19	chr22:30075000-30087000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr22:30075000-30087800	Weak transcription	K562	blood
21	chr22:30075400-30085200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:30075400-30097400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr22:30076000-30085600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:30076800-30096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr22:30077400-30085800	Weak transcription	Colon Smooth Muscle	Colon
26	chr22:30077800-30096400	Weak transcription	Small Intestine	intestine
27	chr22:30079600-30085200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr22:30079600-30097000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr22:30079600-30097400	Weak transcription	Hela-S3	cervix
30	chr22:30079800-30085200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr22:30080000-30085200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr22:30080000-30097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr22:30080200-30085200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr22:30080200-30085200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr22:30080200-30089600	Weak transcription	Colonic Mucosa	Colon
36	chr22:30080200-30098800	Weak transcription	GM12878-XiMat	blood
37	chr22:30080400-30085200	Weak transcription	Brain Germinal Matrix	brain
38	chr22:30080400-30085200	Weak transcription	NHDF-Ad	bronchial
39	chr22:30080400-30085800	Weak transcription	Brain Angular Gyrus	brain
40	chr22:30080400-30087000	Weak transcription	Right Ventricle	heart
41	chr22:30081000-30085600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr22:30081000-30096400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr22:30081200-30085200	Weak transcription	Fetal Lung	lung
44	chr22:30081200-30085600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr22:30081200-30085800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:30081200-30088000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr22:30081200-30088000	Weak transcription	Pancreas	Pancrea
48	chr22:30081200-30096400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr22:30081400-30089000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr22:30081600-30085200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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