Variant report

Variant	rs140124
Chromosome Location	chr22:30143693-30143694
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30135111..30137455-chr22:30141470..30144208,2	K562	blood:
2	chr22:30142692..30145269-chr22:30145289..30147345,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs105311	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs131260	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs131261	0.96[ASN][1000 genomes]
rs131262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs131263	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs131264	0.99[ASN][1000 genomes]
rs131265	1.00[ASN][1000 genomes]
rs131266	1.00[ASN][1000 genomes]
rs131267	0.94[ASN][1000 genomes]
rs131268	0.94[ASN][1000 genomes]
rs131269	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs131270	0.99[ASN][1000 genomes]
rs131271	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs131272	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs131273	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs131274	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131275	0.80[ASN][1000 genomes]
rs131277	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs131279	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs131281	0.94[ASN][1000 genomes]
rs131282	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs131284	0.96[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs131285	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs131286	0.94[ASN][1000 genomes]
rs131287	0.89[ASN][1000 genomes]
rs131289	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs131293	0.82[EUR][1000 genomes]
rs131295	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs131301	0.87[CHB][hapmap]
rs140094	0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs140095	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140096	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140097	0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140099	0.96[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs140100	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140101	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs140103	0.99[ASN][1000 genomes]
rs140104	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140106	0.96[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs140110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[ASN][1000 genomes]
rs140111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs140113	0.96[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140114	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140117	0.93[ASN][1000 genomes]
rs140118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs140119	0.96[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs140121	0.82[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs140122	0.94[ASN][1000 genomes]
rs140123	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs140126	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140127	0.94[ASN][1000 genomes]
rs140128	0.96[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs140129	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs140131	0.94[ASN][1000 genomes]
rs140133	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs140145	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs140147	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs140149	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs140150	0.82[EUR][1000 genomes]
rs17711377	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1894473	0.85[YRI][hapmap]
rs2057882	0.80[EUR][1000 genomes]
rs2074706	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes]
rs2074707	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2079338	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2301402	0.89[CEU][hapmap]
rs249398	0.87[CHB][hapmap]
rs28749829	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs36576	0.87[CHB][hapmap]
rs5752961	0.87[CHB][hapmap]
rs5752964	0.84[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5752978	0.88[YRI][hapmap]
rs5763436	0.81[EUR][1000 genomes]
rs5763512	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs5997529	0.82[EUR][1000 genomes]
rs5997530	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs6006230	0.85[YRI][hapmap]
rs713656	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs713657	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs740041	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs81800	0.87[CHB][hapmap]
rs9306465	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][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	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	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
5	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
6	nsv1065072	chr22:30102176-30155245	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs140124	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30123600-30146800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:30123600-30147000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr22:30125400-30146200	Weak transcription	NHLF	lung
4	chr22:30126000-30144600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr22:30126600-30145200	Strong transcription	Primary T cells from cord blood	blood
6	chr22:30129400-30144600	Strong transcription	Liver	Liver
7	chr22:30130200-30150200	Weak transcription	A549	lung
8	chr22:30130400-30150600	Strong transcription	Fetal Intestine Small	intestine
9	chr22:30130600-30149800	Weak transcription	Psoas Muscle	Psoas
10	chr22:30131000-30145800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr22:30131400-30148600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr22:30131600-30144800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr22:30131600-30145600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr22:30131600-30162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:30131800-30147200	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr22:30133200-30144600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr22:30133400-30144600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr22:30134000-30144600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr22:30134200-30144600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr22:30134400-30144800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:30134400-30158400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr22:30134600-30145200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr22:30136000-30154800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:30136600-30146600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr22:30136600-30146600	Weak transcription	Fetal Heart	heart
26	chr22:30136600-30146800	Weak transcription	Small Intestine	intestine
27	chr22:30136800-30145600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr22:30136800-30146600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr22:30137200-30143800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:30139600-30143800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr22:30139600-30144600	Strong transcription	Brain Angular Gyrus	brain
32	chr22:30139600-30147000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr22:30139800-30144600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr22:30139800-30144800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr22:30139800-30146600	Strong transcription	Lung	lung
36	chr22:30140000-30144600	Strong transcription	Fetal Intestine Large	intestine
37	chr22:30140000-30144600	Strong transcription	Spleen	Spleen
38	chr22:30140000-30144800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr22:30140200-30144600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr22:30140400-30144800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr22:30140600-30144000	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr22:30140600-30144200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr22:30140600-30144600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:30140600-30144800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr22:30140800-30144200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr22:30140800-30144600	Strong transcription	Gastric	stomach
47	chr22:30140800-30144600	Strong transcription	Thymus	Thymus
48	chr22:30140800-30144600	Strong transcription	Dnd41	blood
49	chr22:30141000-30144600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:30141000-30144600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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