Variant report

Variant	rs5753037
Chromosome Location	chr22:30581722-30581723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30580792..30583176-chr22:30587270..30589662,2	K562	blood:
2	chr22:30578652..30582637-chr22:30590732..30593754,4	K562	blood:
3	chr22:30581590..30584656-chr22:30647877..30650932,3	MCF-7	breast:
4	chr22:30580247..30582662-chr22:30589957..30592306,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1468176	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548389	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1807711	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs193471	0.83[AMR][1000 genomes]
rs193474	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs193475	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs193476	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1989870	0.91[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2007446	0.91[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs2007458	0.88[CEU][hapmap]
rs2285667	0.81[AMR][1000 genomes]
rs2412972	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412976	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41161	0.81[AMR][1000 genomes]
rs41165	0.88[CEU][hapmap]
rs41168	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs41171	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs41173	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs41176	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4336042	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820827	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4823076	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753025	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763670	0.81[AMR][1000 genomes]
rs5763751	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5763775	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763779	0.96[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5763790	0.81[EUR][1000 genomes]
rs5763842	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59663694	0.80[AMR][1000 genomes]
rs7287570	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73162764	0.80[AMR][1000 genomes]
rs73164755	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737911	0.92[CEU][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv524628	chr22:30575163-30581722	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 1 diabetes	19430480	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5753037	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs5753037	CABP7	cis	cerebellum	SCAN
rs5753037	TTC28	cis	cerebellum	SCAN
rs5753037	MTMR3	cis	parietal	SCAN
rs5753037	ASCC2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30574400-30583600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr22:30575000-30583600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr22:30575400-30584400	Enhancers	Primary hematopoietic stem cells	blood
4	chr22:30575400-30584800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr22:30575600-30583400	Weak transcription	Primary T cells from cord blood	blood
6	chr22:30575600-30584600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr22:30576200-30588000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr22:30577600-30589600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr22:30577600-30591400	Enhancers	A549	lung
10	chr22:30578000-30585600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr22:30578200-30584800	Weak transcription	Spleen	Spleen
12	chr22:30579000-30585400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr22:30579200-30585400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr22:30579600-30582000	Weak transcription	Fetal Intestine Large	intestine
15	chr22:30579600-30584800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr22:30579600-30591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr22:30579800-30582800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr22:30579800-30585400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr22:30580000-30582200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr22:30580000-30584600	Weak transcription	NHLF	lung
21	chr22:30580000-30585400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr22:30580000-30586400	Weak transcription	Fetal Thymus	thymus
23	chr22:30580000-30588200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:30580200-30582200	Weak transcription	Fetal Lung	lung
25	chr22:30580200-30582200	Weak transcription	HepG2	liver
26	chr22:30580200-30582400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr22:30580200-30586400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr22:30580200-30591400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr22:30580400-30583600	Weak transcription	Osteobl	bone
30	chr22:30580600-30582800	Enhancers	Stomach Mucosa	stomach
31	chr22:30580600-30583000	Enhancers	Fetal Intestine Small	intestine
32	chr22:30580600-30587000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr22:30580800-30583400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr22:30580800-30583600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr22:30580800-30583800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:30581000-30583200	Enhancers	Duodenum Mucosa	Duodenum
37	chr22:30581000-30584400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr22:30581000-30588200	Weak transcription	Dnd41	blood
39	chr22:30581200-30582400	Weak transcription	HSMM	muscle
40	chr22:30581200-30582600	Weak transcription	Small Intestine	intestine
41	chr22:30581200-30583800	Weak transcription	HSMMtube	muscle
42	chr22:30581200-30591400	Weak transcription	Gastric	stomach
43	chr22:30581400-30581800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr22:30581400-30582600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr22:30581400-30582800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr22:30581400-30583000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr22:30581400-30583600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:30581400-30584200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr22:30581400-30584800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr22:30581400-30589600	Weak transcription	Pancreas	Pancrea

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