Variant report

Variant	rs5763670
Chromosome Location	chr22:30383758-30383759
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1548389	0.81[AMR][1000 genomes]
rs1807508	0.86[EUR][1000 genomes]
rs193471	0.83[AMR][1000 genomes]
rs193474	0.88[AMR][1000 genomes]
rs193475	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs193476	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1989870	0.84[AMR][1000 genomes]
rs2007446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007458	0.88[EUR][1000 genomes]
rs2285667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412972	0.85[AMR][1000 genomes]
rs3747149	0.85[EUR][1000 genomes]
rs3747150	0.84[EUR][1000 genomes]
rs3788420	0.89[EUR][1000 genomes]
rs41155	0.81[EUR][1000 genomes]
rs41156	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41157	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41159	0.86[EUR][1000 genomes]
rs41161	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41168	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41170	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41171	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41173	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41176	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4820827	0.84[AMR][1000 genomes]
rs4823076	0.87[AMR][1000 genomes]
rs5752978	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752992	0.89[EUR][1000 genomes]
rs5753037	0.81[AMR][1000 genomes]
rs5763592	0.83[AFR][1000 genomes]
rs5763614	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763638	0.85[EUR][1000 genomes]
rs5763645	0.87[EUR][1000 genomes]
rs5763646	0.81[EUR][1000 genomes]
rs5763649	0.87[EUR][1000 genomes]
rs5763650	0.86[EUR][1000 genomes]
rs5763651	0.86[EUR][1000 genomes]
rs5763671	0.89[EUR][1000 genomes]
rs5763688	0.87[EUR][1000 genomes]
rs5763751	0.84[AMR][1000 genomes]
rs5763775	0.87[AMR][1000 genomes]
rs5763779	0.80[AMR][1000 genomes]
rs59663694	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997549	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6006288	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7285583	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7287570	0.87[AMR][1000 genomes]
rs7289604	0.84[EUR][1000 genomes]
rs73162764	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737908	0.88[EUR][1000 genomes]
rs737911	0.85[EUR][1000 genomes]
rs737939	0.80[EUR][1000 genomes]
rs9306468	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs960987	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9614100	0.91[AFR][1000 genomes]
rs997913	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv3591	chr22:30344208-30388897	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5763670	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30348400-30387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
3	chr22:30351200-30385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr22:30351200-30387400	Weak transcription	Ovary	ovary
5	chr22:30352800-30388600	Weak transcription	HepG2	liver
6	chr22:30354600-30390200	Weak transcription	Colonic Mucosa	Colon
7	chr22:30354800-30390400	Weak transcription	Small Intestine	intestine
8	chr22:30358800-30387400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr22:30366000-30384200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr22:30366400-30387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30366600-30390800	Weak transcription	Gastric	stomach
13	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr22:30368400-30387400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr22:30369400-30388400	Weak transcription	NH-A	brain
17	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
18	chr22:30370200-30388400	Weak transcription	NHLF	lung
19	chr22:30370600-30390800	Weak transcription	Right Ventricle	heart
20	chr22:30370800-30387400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr22:30370800-30390000	Weak transcription	Stomach Mucosa	stomach
22	chr22:30371800-30385800	Weak transcription	Lung	lung
23	chr22:30371800-30386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:30373400-30388600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr22:30373600-30388600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr22:30374200-30389600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr22:30375200-30386000	Weak transcription	Thymus	Thymus
29	chr22:30375200-30389800	Weak transcription	K562	blood
30	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr22:30375400-30390800	Weak transcription	Pancreas	Pancrea
32	chr22:30375800-30387400	Weak transcription	Spleen	Spleen
33	chr22:30375800-30388400	Weak transcription	A549	lung
34	chr22:30375800-30389800	Weak transcription	HUVEC	blood vessel
35	chr22:30376000-30387200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr22:30376000-30387400	Weak transcription	Brain Germinal Matrix	brain
37	chr22:30376000-30387400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr22:30376000-30387400	Weak transcription	Colon Smooth Muscle	Colon
39	chr22:30376000-30387400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr22:30376200-30388200	Weak transcription	HMEC	breast
41	chr22:30376200-30389800	Weak transcription	Hela-S3	cervix
42	chr22:30376200-30394800	Weak transcription	GM12878-XiMat	blood
43	chr22:30376400-30384000	Strong transcription	Fetal Stomach	stomach
44	chr22:30376400-30386000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr22:30376600-30386000	Weak transcription	Left Ventricle	heart
46	chr22:30376600-30387400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr22:30376600-30387400	Weak transcription	Psoas Muscle	Psoas
48	chr22:30376800-30387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:30377000-30387400	Weak transcription	Fetal Thymus	thymus
50	chr22:30377000-30389400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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