Variant report

Variant	rs9306465
Chromosome Location	chr22:30221826-30221827
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30153529..30155692-chr22:30219778..30222690,2	K562	blood:

Variant related genes	Relation type
ENSG00000200976	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs105311	0.87[CHB][hapmap]
rs1138120	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs131260	0.88[CHB][hapmap]
rs131262	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs131269	0.82[AMR][1000 genomes]
rs131271	0.87[CHB][hapmap]
rs131272	0.87[CHB][hapmap]
rs131273	0.87[CHB][hapmap]
rs131274	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs131277	0.88[CHB][hapmap]
rs131279	0.88[CHB][hapmap]
rs131282	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs131284	0.84[CHB][hapmap]
rs131285	0.87[CHB][hapmap]
rs131289	0.82[AMR][1000 genomes]
rs131293	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131295	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs140095	0.86[AMR][1000 genomes]
rs140096	0.88[CHB][hapmap]
rs140097	0.83[CHB][hapmap]
rs140099	0.84[CHB][hapmap]
rs140100	0.88[CHB][hapmap]
rs140101	0.87[CHB][hapmap]
rs140102	0.88[CHB][hapmap]
rs140104	0.83[CHB][hapmap]
rs140106	0.84[CHB][hapmap]
rs140107	0.88[CHB][hapmap]
rs140110	0.88[CHB][hapmap]
rs140111	0.88[CHB][hapmap]
rs140113	0.84[CHB][hapmap]
rs140114	0.83[CHB][hapmap]
rs140118	0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs140119	0.84[CHB][hapmap]
rs140120	0.87[CHB][hapmap]
rs140121	0.84[CHB][hapmap]
rs140123	0.87[CHB][hapmap]
rs140124	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs140126	0.83[CHB][hapmap]
rs140128	0.84[CHB][hapmap]
rs140129	0.87[CHB][hapmap]
rs140133	0.87[CHB][hapmap]
rs140145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140147	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs140149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140150	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17711377	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1894473	1.00[YRI][hapmap]
rs2007446	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2057882	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074706	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2079338	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301402	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs249398	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28749829	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36574	0.96[ASN][1000 genomes]
rs36576	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3958027	0.86[AMR][1000 genomes]
rs41168	0.92[CEU][hapmap]
rs5752961	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs5752964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752978	0.89[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs5763512	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997529	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997530	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997534	0.81[EUR][1000 genomes]
rs5997535	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997549	0.86[AMR][1000 genomes]
rs6006267	0.85[CEU][hapmap]
rs6006274	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6006288	0.86[AMR][1000 genomes]
rs6006315	1.00[YRI][hapmap]
rs713656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713657	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7287434	0.81[AMR][1000 genomes]
rs737911	0.89[CEU][hapmap]
rs737945	0.86[CEU][hapmap]
rs740041	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs81800	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9306468	0.86[CEU][hapmap]
rs9614055	0.99[ASN][1000 genomes]
rs9614077	0.86[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
rs9306465	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	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
3	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
4	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
5	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr22:30195400-30222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr22:30195400-30222200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:30197000-30222200	Strong transcription	Dnd41	blood
17	chr22:30199200-30222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr22:30205800-30222000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
21	chr22:30208800-30231200	Strong transcription	Lung	lung
22	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:30209000-30227600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr22:30212400-30222000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr22:30212400-30222000	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr22:30213000-30222000	Strong transcription	Ovary	ovary
28	chr22:30213600-30223200	Weak transcription	Esophagus	oesophagus
29	chr22:30213600-30226000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr22:30215000-30230800	Strong transcription	Fetal Brain Female	brain
31	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:30216400-30226200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr22:30217000-30222000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr22:30217000-30222000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr22:30217200-30222000	Strong transcription	Colon Smooth Muscle	Colon
36	chr22:30218000-30225000	Strong transcription	Fetal Intestine Large	intestine
37	chr22:30218000-30230600	Strong transcription	Fetal Thymus	thymus
38	chr22:30218000-30231000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr22:30218200-30222000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr22:30218200-30222000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr22:30218200-30222000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr22:30218200-30232200	Strong transcription	Fetal Intestine Small	intestine
43	chr22:30218400-30222000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:30218400-30222000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr22:30218400-30222000	Strong transcription	Fetal Lung	lung
46	chr22:30218400-30222000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr22:30218400-30222000	Strong transcription	NH-A	brain
48	chr22:30218400-30222000	Strong transcription	NHLF	lung
49	chr22:30218400-30222200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:30218400-30222200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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