Variant report

Variant	rs9306468
Chromosome Location	chr22:30374281-30374282
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	chr22:30366853..30371460-chr22:30371891..30375827,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1076135	0.83[CEU][hapmap]
rs140145	0.92[CEU][hapmap]
rs140147	1.00[CEU][hapmap]
rs140149	0.92[CEU][hapmap]
rs1548389	0.96[CEU][hapmap]
rs1989870	1.00[CEU][hapmap]
rs2007446	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2007458	0.93[CEU][hapmap]
rs2074706	0.83[CEU][hapmap]
rs2074707	0.83[CEU][hapmap]
rs2285667	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301402	0.86[CEU][hapmap]
rs3788420	0.80[EUR][1000 genomes]
rs3958027	0.86[AFR][1000 genomes]
rs41155	0.81[EUR][1000 genomes]
rs41156	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41157	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41161	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41165	0.93[CEU][hapmap]
rs41168	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41170	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41171	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41173	1.00[CEU][hapmap]
rs5752964	0.89[CEU][hapmap]
rs5752975	0.93[CEU][hapmap]
rs5752978	1.00[CEU][hapmap]
rs5752992	0.80[EUR][1000 genomes]
rs5763512	0.83[CEU][hapmap]
rs5763614	0.84[EUR][1000 genomes]
rs5763670	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5763671	0.80[EUR][1000 genomes]
rs5763775	0.96[CEU][hapmap]
rs5763779	1.00[CEU][hapmap];0.93[AFR][1000 genomes]
rs59663694	0.88[EUR][1000 genomes]
rs5997530	0.83[CEU][hapmap]
rs713656	0.86[CEU][hapmap]
rs713657	0.83[CEU][hapmap]
rs7285583	0.80[EUR][1000 genomes]
rs73162764	0.87[EUR][1000 genomes]
rs737911	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740041	0.83[CEU][hapmap]
rs9306465	0.86[CEU][hapmap]
rs960987	0.85[EUR][1000 genomes]
rs9614077	0.86[AFR][1000 genomes]
rs9614102	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs997913	0.93[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv3591	chr22:30344208-30388897	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9306468	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30334200-30374800	Weak transcription	Thymus	Thymus
2	chr22:30340200-30374800	Weak transcription	Fetal Thymus	thymus
3	chr22:30340600-30375000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr22:30340800-30376000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr22:30342600-30375200	Weak transcription	Spleen	Spleen
6	chr22:30344200-30375000	Weak transcription	HMEC	breast
7	chr22:30344400-30376000	Weak transcription	HSMMtube	muscle
8	chr22:30344600-30374600	Weak transcription	Adipose Nuclei	Adipose
9	chr22:30344600-30375600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr22:30345000-30375400	Weak transcription	Fetal Brain Female	brain
11	chr22:30345400-30379000	Weak transcription	Esophagus	oesophagus
12	chr22:30348000-30374800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr22:30348400-30387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr22:30350600-30375400	Weak transcription	GM12878-XiMat	blood
15	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
16	chr22:30351200-30385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr22:30351200-30387400	Weak transcription	Ovary	ovary
18	chr22:30352800-30388600	Weak transcription	HepG2	liver
19	chr22:30353600-30375000	Weak transcription	Psoas Muscle	Psoas
20	chr22:30354600-30390200	Weak transcription	Colonic Mucosa	Colon
21	chr22:30354800-30390400	Weak transcription	Small Intestine	intestine
22	chr22:30355000-30374400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:30356200-30376600	Weak transcription	Fetal Kidney	kidney
24	chr22:30358800-30374800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:30358800-30387400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr22:30359000-30374800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr22:30359400-30375600	Weak transcription	Fetal Lung	lung
28	chr22:30360600-30374800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr22:30361400-30375000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:30363200-30375600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr22:30363600-30375000	Weak transcription	Fetal Intestine Large	intestine
33	chr22:30364200-30374600	Weak transcription	Liver	Liver
34	chr22:30364200-30374800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr22:30364200-30374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr22:30365200-30374600	Weak transcription	NHEK	skin
37	chr22:30366000-30384200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr22:30366400-30387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr22:30366600-30374400	Weak transcription	NHDF-Ad	bronchial
40	chr22:30366600-30374800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr22:30366600-30390800	Weak transcription	Gastric	stomach
42	chr22:30366800-30375600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr22:30366800-30376000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr22:30367000-30375600	Weak transcription	Colon Smooth Muscle	Colon
45	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr22:30368000-30375400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr22:30368400-30374600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr22:30368400-30374800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr22:30368400-30374800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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