Variant report

Variant	rs28749829
Chromosome Location	chr22:30219326-30219327
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	chr22:30218800..30221141-chr22:30232734..30234943,2	MCF-7	breast:
2	chr22:30218166..30221158-chr22:30224343..30226322,2	K562	blood:

Variant related genes	Relation type
ENSG00000100325	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1138120	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs131269	0.82[AMR][1000 genomes]
rs131274	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs131289	0.82[AMR][1000 genomes]
rs131293	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131295	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131301	0.98[ASN][1000 genomes]
rs140095	0.86[AMR][1000 genomes]
rs140118	0.83[AMR][1000 genomes]
rs140124	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs140145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs140147	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs140149	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140150	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17711377	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057882	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074706	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074707	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079338	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301402	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs249398	0.99[ASN][1000 genomes]
rs36574	0.95[ASN][1000 genomes]
rs36576	0.99[ASN][1000 genomes]
rs3958027	0.86[AMR][1000 genomes]
rs5752961	0.98[ASN][1000 genomes]
rs5752964	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752978	0.82[AMR][1000 genomes]
rs5763512	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997529	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997530	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997535	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997549	0.86[AMR][1000 genomes]
rs6006274	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6006288	0.86[AMR][1000 genomes]
rs713656	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713657	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7287434	0.81[AMR][1000 genomes]
rs740041	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs81800	0.98[ASN][1000 genomes]
rs9306465	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9614055	0.98[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
rs28749829	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	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr22:30195400-30222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:30195400-30222200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr22:30196200-30222200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr22:30196400-30221200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr22:30197000-30222200	Strong transcription	Dnd41	blood
19	chr22:30199200-30222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr22:30205800-30222000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr22:30206000-30221800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr22:30206000-30221800	Strong transcription	Brain Anterior Caudate	brain
24	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
25	chr22:30208800-30231200	Strong transcription	Lung	lung
26	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr22:30209000-30220200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr22:30209000-30227600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr22:30211000-30220200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr22:30211800-30219800	Weak transcription	Small Intestine	intestine
32	chr22:30212400-30221800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr22:30212400-30221800	Strong transcription	Brain Hippocampus Middle	brain
34	chr22:30212400-30222000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr22:30212400-30222000	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr22:30213000-30221800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr22:30213000-30222000	Strong transcription	Ovary	ovary
38	chr22:30213400-30221800	Strong transcription	HSMMtube	muscle
39	chr22:30213600-30220400	Weak transcription	Psoas Muscle	Psoas
40	chr22:30213600-30223200	Weak transcription	Esophagus	oesophagus
41	chr22:30213600-30226000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr22:30214600-30221600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr22:30214600-30221600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr22:30215000-30230800	Strong transcription	Fetal Brain Female	brain
45	chr22:30215200-30221600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr22:30215400-30220400	Weak transcription	Pancreas	Pancrea
48	chr22:30215400-30221600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr22:30215600-30221600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr22:30216000-30220000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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