Variant report

Variant	rs2252472
Chromosome Location	chr22:30064117-30064118
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	chr22:30063718..30066289-chr22:30068582..30070732,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1034880	0.86[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs1476757	0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs2071622	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245415	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267150	0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2267151	0.85[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2283863	0.86[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2283864	0.95[AFR][1000 genomes]
rs2527337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530667	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2530668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530669	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530672	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2530673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530675	0.86[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2530676	0.90[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2531850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857637	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2857641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857642	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2857645	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857648	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2857650	0.86[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2857651	0.80[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs5752953	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs5763409	0.98[AFR][1000 genomes]
rs5763422	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs5763431	0.94[AFR][1000 genomes]
rs7291645	0.85[JPT][hapmap];0.80[AFR][1000 genomes]
rs737931	0.86[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9608806	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2252472	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs2252472	NIPSNAP1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 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	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
4	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
5	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
6	chr22:30037200-30064200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:30038800-30069800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr22:30039000-30068000	Weak transcription	Hela-S3	cervix
9	chr22:30048000-30064200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:30050200-30075000	Strong transcription	Stomach Smooth Muscle	stomach
11	chr22:30050200-30084800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr22:30050400-30084400	Strong transcription	Left Ventricle	heart
13	chr22:30050400-30093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:30050800-30084800	Strong transcription	Thymus	Thymus
15	chr22:30051000-30083600	Strong transcription	Fetal Muscle Leg	muscle
16	chr22:30051000-30085400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr22:30051400-30082600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr22:30053200-30065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30053400-30084400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr22:30053400-30087400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr22:30053800-30081000	Strong transcription	Fetal Intestine Large	intestine
22	chr22:30053800-30084600	Strong transcription	Fetal Stomach	stomach
23	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr22:30054400-30065200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr22:30054400-30067800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:30055400-30070800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
28	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr22:30056200-30070800	Weak transcription	Fetal Kidney	kidney
30	chr22:30056200-30084600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr22:30056200-30084800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr22:30056400-30064400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr22:30056400-30066600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr22:30056400-30084600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:30056800-30066400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr22:30057800-30064400	Weak transcription	A549	lung
37	chr22:30057800-30085600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr22:30057800-30086000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr22:30058200-30084200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr22:30058800-30069200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr22:30059000-30064200	Weak transcription	Psoas Muscle	Psoas
42	chr22:30059200-30064200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr22:30059600-30081800	Strong transcription	NHLF	lung
44	chr22:30060000-30084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr22:30060200-30093600	Strong transcription	Fetal Thymus	thymus
46	chr22:30060600-30081600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr22:30061000-30064200	Weak transcription	Brain Anterior Caudate	brain
48	chr22:30061000-30064200	Weak transcription	Brain Substantia Nigra	brain
49	chr22:30061000-30064200	Weak transcription	Fetal Brain Female	brain
50	chr22:30061000-30064200	Weak transcription	Pancreas	Pancrea

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