Variant report

Variant	rs1548389
Chromosome Location	chr22:30573552-30573553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30572974..30575088-chr22:30642286..30645373,3	MCF-7	breast:
2	chr22:30566597..30569534-chr22:30572509..30574733,2	K562	blood:
3	chr22:30573019..30575061-chr22:30649550..30652026,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128342	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1468176	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1807711	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs193471	0.83[AMR][1000 genomes]
rs193474	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193475	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs193476	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1989870	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2007446	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs2007458	0.89[CEU][hapmap]
rs2285667	0.81[AMR][1000 genomes]
rs2412972	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412976	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41161	0.81[AMR][1000 genomes]
rs41165	0.89[CEU][hapmap]
rs41168	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs41171	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs41173	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs41176	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4336042	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820827	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823076	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753008	0.81[EUR][1000 genomes]
rs5753025	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5753037	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763670	0.81[AMR][1000 genomes]
rs5763751	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763775	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763779	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5763790	0.84[EUR][1000 genomes]
rs5763842	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59663694	0.80[AMR][1000 genomes]
rs7287570	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73162764	0.80[AMR][1000 genomes]
rs73164755	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs737911	0.96[CEU][hapmap]
rs9306468	0.96[CEU][hapmap]
rs997913	0.89[CEU][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1548389	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30566400-30573600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr22:30566600-30573800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr22:30569200-30574400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr22:30571600-30573800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr22:30571600-30574400	Enhancers	Primary hematopoietic stem cells	blood
6	chr22:30571600-30574800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr22:30572000-30574000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr22:30572000-30574200	Weak transcription	A549	lung
9	chr22:30572000-30575400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr22:30572000-30577400	Weak transcription	Fetal Intestine Small	intestine
11	chr22:30572200-30574200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:30572200-30574200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr22:30572200-30575600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr22:30572200-30576200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:30572800-30573800	Weak transcription	Fetal Thymus	thymus
16	chr22:30572800-30578000	Weak transcription	Spleen	Spleen
17	chr22:30572800-30579000	Weak transcription	Fetal Brain Male	brain
18	chr22:30573000-30573600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:30573200-30575000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:30573200-30575400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr22:30573200-30576400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr22:30573400-30573600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr22:30573400-30575000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr22:30573400-30575000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr22:30573400-30575400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr22:30573400-30575600	Enhancers	Primary T cells from cord blood	blood
27	chr22:30573400-30575600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr22:30573400-30575600	Enhancers	Thymus	Thymus
29	chr22:30573400-30575800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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